Align Lmo2663 protein (characterized, see rationale)
to candidate N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Dyella79:N515DRAFT_0039 Length = 344 Score = 151 bits (382), Expect = 2e-41 Identities = 109/344 (31%), Positives = 179/344 (52%), Gaps = 12/344 (3%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTT---PV 57 MKA+VK P + +++V P+V ++V IK+ T ICG+D+H +K + + T + Sbjct: 5 MKALVKRLPEQG-IWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIKPGL 63 Query: 58 TLGHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQAN 117 T+GHEF G +V++GP VT KVGDRV++E CG C C+ +LC N GIG N Sbjct: 64 TIGHEFVGRIVDIGPGVTGYKVGDRVSAEGHI-VCGHCRNCRAGRQHLCPNTVGIGVNRN 122 Query: 118 GSFAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIG 177 G+FAE++ + + ++I E AA +P H ALE I D VL+ G GPIG Sbjct: 123 GAFAEYMTMPASNLWPIPDQIPSELAAFFDPYGNAAHCALEFDLIGED--VLITGAGPIG 180 Query: 178 LLLAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAER 237 ++ A + K GA ++ D RL+LA ++G R+V+ + L +VV + G + Sbjct: 181 IIAAGIAKHVGARNVVVTDVNDY-RLKLAADMGATRVVNVANQSLRDVVKDL-HIEGFDV 238 Query: 238 VFDCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKP-SS 296 + SG A N L G +G+ + ID + +I + + G ++ + Sbjct: 239 GLEMSGNPRAFNDMLDCMYHGGKIALLGIM-PRGAGIDWDKVIFKGLTLQGIYGRRMYET 297 Query: 297 WILALDLLANGKIDTDKMITKVYGLDDWREAFEAVMAGNEIKVL 340 W ++ +G K++T +DD+++ F+ + AG+ KV+ Sbjct: 298 WYKMTQMVLSG-FPLQKVLTHQIHIDDFQKGFDLMDAGHCGKVV 340 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: 324 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