Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate WP_048080142.1 EJ01_RS01405 hypothetical protein
Query= curated2:Q82MN2 (342 letters) >NCBI__GCF_000745485.1:WP_048080142.1 Length = 399 Score = 100 bits (249), Expect = 6e-26 Identities = 93/317 (29%), Positives = 146/317 (46%), Gaps = 54/317 (17%) Query: 1 MKALVKEKAEPGLWLMDVPEPEIG-PGDVLIKVLRTGICGTDLHIRSWDGWAQQAVRTPL 59 MKA+V K + + DV P+I P D ++++ + ICG+DLH+ +DG + + Sbjct: 1 MKAVVY-KGPKNVEVEDVENPKISKPTDAIVRITSSAICGSDLHM--YDG--ETTFESGR 55 Query: 60 VLGHEFVGEVVETGRDVVDIKAGDRVSGEGHLVCGKCRNCQAGRRHLCRAT--------- 110 LGHE +G V E G V +K GDRV ++ CG C NC G + C Sbjct: 56 TLGHEPMGVVEEVGDAVQLVKPGDRVVMPFNIACGFCLNCIQGLTNACLTLNPDQPGSAY 115 Query: 111 --VGLGVGRDGAFAEYVALPAANVWVHRVP------VDLDVAAIFDPFGNAVH-TALSFP 161 V +G + G AEYV +P A+ ++P + D + D F + + T L+ Sbjct: 116 GYVNMGPYQGGQ-AEYVLVPYADWACLKLPGEPGDEFEDDFVLLADIFPTSYYSTELANV 174 Query: 162 LVGEDVLITGAGPIGLMAAAVARHAGARNVMITDVSEERLELARKIGVSLALNVADTTIA 221 +G+ V + GAGP+GL+AA A GA V I D SEERL+ A IG ++ +N D A Sbjct: 175 SIGKAVAVFGAGPVGLLAAYSAILKGASEVYIIDDSEERLKRAESIG-AIPINTDDGDPA 233 Query: 222 D-------------------GQRALGLREGFD-IGLE--------MSGRPEAMRDMIANM 253 ++ LG+ D +G + R + + D+ + Sbjct: 234 QQIMEIRQNNKNLMESLRPGEEKTLGVDSAIDAVGFQAYDRDNPNQEKRNQVLMDIANVI 293 Query: 254 THGGRIAMLGLPSQEFP 270 GG + ++G+ +E P Sbjct: 294 NAGGHVGLIGVYPKENP 310 Lambda K H 0.322 0.140 0.431 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: 316 Number of extensions: 13 Number of successful extensions: 3 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: 342 Length of database: 399 Length adjustment: 30 Effective length of query: 312 Effective length of database: 369 Effective search space: 115128 Effective search space used: 115128 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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