Align Lmo2663 protein (characterized, see rationale)
to candidate SMc01564 SMc01564 L-threonine 3-dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Smeli:SMc01564 Length = 344 Score = 173 bits (439), Expect = 5e-48 Identities = 123/347 (35%), Positives = 184/347 (53%), Gaps = 15/347 (4%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEY---KNPTTPV 57 MKA+VKT P + ++ V P++ + V I+V + ICG+D+H + + K P+ Sbjct: 5 MKALVKTKPEVG-LWMERVPVPEIGPNDVLIRVRKSAICGTDVHIWNWDQWAEKTIPVPM 63 Query: 58 TLGHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQAN 117 +GHEF G VVEVGP V+ VG+RV+ E CG+C C+ +LC N G+G Sbjct: 64 VVGHEFMGEVVEVGPAVSKHHVGERVSGEGHI-VCGKCRNCRAGRGHLCRNTLGVGVNRP 122 Query: 118 GSFAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIG 177 GSFAEFV E + + + + E AA+ +P VH+AL + D VLV G GPIG Sbjct: 123 GSFAEFVCLPEYNVVSIPDDVPDEIAAIFDPFGNAVHTALSFDLVGED--VLVTGAGPIG 180 Query: 178 LLLAQVVKAQGA-TVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEV--VLGMTGGYG 234 ++ A V K GA V++ I + RL LA++LG+D +VD KE LA+V V+GMT G+ Sbjct: 181 IMGAMVAKRCGARKVVITDI--NPVRLDLARKLGIDHVVDASKEKLADVMRVIGMTEGFD 238 Query: 235 AERVFDCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP 294 + SGA PA + G +G+ A ID +I + + G ++ Sbjct: 239 VG--LEMSGAAPAFRDMIDKMNNGGKIAILGI-APAGFEIDWNKVIFKMLNLKGIYGREM 295 Query: 295 SSWILALDLLANGKIDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341 + G +D +IT G+DD+R+ FEA+ +GN KV++ Sbjct: 296 FETWYKMIAFVQGGLDLSPIITHRIGIDDFRDGFEAMRSGNSGKVVM 342 Lambda K H 0.317 0.135 0.392 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: 318 Number of extensions: 20 Number of successful extensions: 6 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: 343 Length of database: 344 Length adjustment: 29 Effective length of query: 314 Effective length of database: 315 Effective search space: 98910 Effective search space used: 98910 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: 49 (23.5 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