Align Lactate utilization protein A (characterized)
to candidate WP_028314524.1 G491_RS0110190 (Fe-S)-binding protein
Query= SwissProt::O07020 (238 letters) >NCBI__GCF_000429905.1:WP_028314524.1 Length = 243 Score = 218 bits (555), Expect = 9e-62 Identities = 106/234 (45%), Positives = 147/234 (62%), Gaps = 1/234 (0%) Query: 3 VSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMKRM 62 +SL + CL++MF GK+ V LLERL + E Q CCG PA N+G++ +A+K K Sbjct: 4 ISLHIPCLMNMFMPKTGKSVVRLLERLDVPFVYHEDQTCCGLPASNAGFLPEARKVAKHF 63 Query: 63 IETFQDSEYVVSPSGSCTTMFRE-YPHLFQDDPKWADKAKKLADKTYELTDFIVNVLGVE 121 +E F D VVSPSGSC M + YP LF+D+P+W +A+ +A KTYE T ++V++LG+E Sbjct: 64 MEVFGDDPVVVSPSGSCVEMITQRYPALFEDEPEWKARAQDMASKTYEFTQYLVDILGIE 123 Query: 122 DVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGFGGTFSVKM 181 D G K H SC + R LGV ++P KL++ VKG + + CCGFGG FS K Sbjct: 124 DAGGKFSGKVAYHESCSLLRGLGVSEQPKKLIASVKGAELVPMQNADVCCGFGGEFSHKY 183 Query: 182 AQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVMHIAEVL 235 ++ISE MV EKV +GA+VL+ + GC +NI G + R KVMHIA++L Sbjct: 184 SEISETMVQEKVTNFINSGADVLVMGEPGCFLNISGYVSRNHPGRKVMHIADLL 237 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: 167 Number of extensions: 9 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: 238 Length of database: 243 Length adjustment: 23 Effective length of query: 215 Effective length of database: 220 Effective search space: 47300 Effective search space used: 47300 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 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