Align Lmo2663 protein (characterized, see rationale)
to candidate 7026976 Shewana3_4105 L-threonine 3-dehydrogenase (RefSeq)
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__ANA3:7026976 Length = 341 Score = 152 bits (385), Expect = 9e-42 Identities = 106/333 (31%), Positives = 178/333 (53%), Gaps = 16/333 (4%) Query: 16 LKDVEEPQVYGDKVKIKVAFTGICGSDIHTFK-GEYKNPTTPVTL--GHEFSGVVVEVGP 72 L D +P++ + + IK+ T ICG+D+H + E+ T PV + GHE+ G VV++G Sbjct: 15 LVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMVVGHEYVGEVVDIGQ 74 Query: 73 DVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGSFAEFVLSREESCH 132 +V K+GDRV+ E TCG C C+ +LC N G+G GSFAE+++ + Sbjct: 75 EVRGFKIGDRVSGEGHI-TCGHCRNCRAGRTHLCRNTSGVGVNREGSFAEYLVIPAFNAF 133 Query: 133 VLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLLLAQVVKAQGATVI 192 + + IS + A++ +P VH+AL + D VL+ G GPIG++ A V + GA + Sbjct: 134 KIPDDISDDLASIFDPFGNAVHTALSFDLVGED--VLITGAGPIGIMAAAVCRHVGARHV 191 Query: 193 MAGITKDSD-RLRLAKELGMDRIVDTLKEDLAEVV--LGMTGGYGAERVFDCSGAVPAVN 249 + IT ++ RL LA+++G R V+ +E L +V+ LGMT G+ + SG A + Sbjct: 192 V--ITDVNEYRLELARKMGATRAVNVAQESLKDVMKELGMTEGFDVG--LEMSGVPSAFH 247 Query: 250 QGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP-SSWILALDLLANGK 308 L G +G+ + AID +I + + G ++ +W L+ +G Sbjct: 248 AMLDTMNHGGKIAMLGI-PGGEMAIDWSKVIFKGLVIKGIYGREMFETWYKMASLIQSG- 305 Query: 309 IDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341 +D +IT Y +DD+++ F+A+ +G KV++ Sbjct: 306 LDISPIITHHYKIDDFQKGFDAMGSGQSGKVIL 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: 297 Number of extensions: 19 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: 341 Length adjustment: 29 Effective length of query: 314 Effective length of database: 312 Effective search space: 97968 Effective search space used: 97968 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