Align Lmo2663 protein (characterized, see rationale)
to candidate H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Burk376:H281DRAFT_03586 Length = 343 Score = 150 bits (379), Expect = 5e-41 Identities = 106/348 (30%), Positives = 181/348 (52%), Gaps = 17/348 (4%) Query: 1 MKAVVKTN--PGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGE---YKNPTT 55 MKA+ K PG + L DV+ P+V + V I++ T ICG+DIH +K + K Sbjct: 1 MKALAKLERAPG---LTLTDVKVPEVGHNDVMIRIKRTAICGTDIHIWKWDDWAQKTIPV 57 Query: 56 PVTLGHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQ 115 P+ +GHE+ G +VE+G +V +GDRV+ E TCG C C+ +LC N G+G Sbjct: 58 PMHVGHEYVGEIVEMGAEVRGFSIGDRVSGEGHI-TCGFCRNCRAGRRHLCRNTVGVGVN 116 Query: 116 ANGSFAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGP 175 G+FAE+++ + + IS + AA+ +P H+AL + D VL+ G GP Sbjct: 117 REGAFAEYLVIPAFNAFKIPPEISDDLAAIFDPFGNATHTALSFNLVGED--VLITGAGP 174 Query: 176 IGLLLAQVVKAQGATVIMAGITKDSD-RLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYG 234 IG++ + K GA ++ IT +D RL LA+++G R V+ +E L +V+ + G Sbjct: 175 IGIMAVAIAKHVGARNVV--ITDINDYRLGLARKMGATRAVNVSRESLRDVMADLHMAEG 232 Query: 235 AERVFDCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP 294 + + SG VP G+ G + + + AID +I + + G ++ Sbjct: 233 FDVGLEMSG-VPGAFTGMLEAMNHGGKIALLGIPPAQTAIDWNQVIFKGLEIKGIYGREM 291 Query: 295 -SSWILALDLLANGKIDTDKMITKVYGLDDWREAFEAVMAGNEIKVLV 341 +W + +L +G +D ++T + +DD+++AF +++G KV++ Sbjct: 292 FETWYKMVAMLQSG-LDLSPILTHHFKVDDYQQAFATMLSGESGKVIL 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: 285 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: 343 Length adjustment: 29 Effective length of query: 314 Effective length of database: 314 Effective search space: 98596 Effective search space used: 98596 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