Align Lmo2663 protein (characterized, see rationale)
to candidate RR42_RS22860 RR42_RS22860 l-threonine 3-dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Cup4G11:RR42_RS22860 Length = 351 Score = 147 bits (371), Expect = 4e-40 Identities = 109/348 (31%), Positives = 178/348 (51%), Gaps = 17/348 (4%) Query: 1 MKAVVKTN--PGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFK-GEYKNPTTPV 57 MKA+ K PG + L DV EP+V + V I++ T ICG+DIH +K E+ T PV Sbjct: 1 MKALAKLERAPG---LTLTDVPEPEVGHNDVMIRIRQTAICGTDIHIWKWDEWAQNTIPV 57 Query: 58 TL--GHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQ 115 + GHE+ G +V +G +V + +GDRV+ E TCG C C+ +LC N G+G Sbjct: 58 PMQVGHEYVGEIVAIGQEVRGLAIGDRVSGEGHI-TCGFCRNCRAGRRHLCRNSVGVGVN 116 Query: 116 ANGSFAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGP 175 G+FAE+++ + + + I E AA+ +P H+AL + D VL+ G GP Sbjct: 117 RAGAFAEYLVIPAFNAFRIPDDIPDEIAAIFDPFGNATHTALSFNLVGED--VLITGAGP 174 Query: 176 IGLLLAQVVKAQGA-TVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYG 234 IG++ A + + GA V++ + + RL LA+++G R V+ E+L +V + G Sbjct: 175 IGIMAAAIARHVGARNVVITDV--NEYRLALARKMGATRAVNVQHENLKDVAAELHMTEG 232 Query: 235 AERVFDCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP 294 + + SG A L G +G+ K AID +I + + G ++ Sbjct: 233 FDVGMEMSGVPTAFATMLEHMNHGGKIAMLGI-PPSKMAIDWNQVIFKGLEIKGIYGREM 291 Query: 295 -SSWILALDLLANGKIDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341 +W + +L +G +D MIT + + D+ F A+++GN KV++ Sbjct: 292 FETWYKMVAMLQSG-LDLTPMITHRFRVGDFEAGFAAMLSGNSGKVVL 338 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: 274 Number of extensions: 13 Number of successful extensions: 5 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: 351 Length adjustment: 29 Effective length of query: 314 Effective length of database: 322 Effective search space: 101108 Effective search space used: 101108 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