Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate HSERO_RS17015 HSERO_RS17015 sulfurtransferase
Query= reanno::Phaeo:GFF3379 (342 letters) >FitnessBrowser__HerbieS:HSERO_RS17015 Length = 345 Score = 143 bits (361), Expect = 6e-39 Identities = 104/345 (30%), Positives = 169/345 (48%), Gaps = 10/345 (2%) Query: 1 MKALEKSHPREGLWMVQAPVPE-IGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPM 59 M+AL RE L + + +P+ +G +V I+I T GICG+D+H + V PM Sbjct: 1 MQALVLEATRE-LKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPM 59 Query: 60 ITGHEFAGEIVEIGRNVTDLAVGQRCSGEGHLIQTDSRQSRAGKFHLDPGTRGIGVNE-Q 118 + GHE +G ++E+G V+ L VG R E + + DS + G ++LDP R Sbjct: 60 VLGHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIH 119 Query: 119 GAFAQYLKLPAFNVVPLPEDIPDEIGAILDPLGNAVHTALSFDLL-GEDVLITGAGPIGV 177 G + PA LP+++ GAI++PL + A + G+ ++ GAG IG Sbjct: 120 GCLTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVIGAGTIGA 179 Query: 178 MAAAVARHAGARHVVITDINPDRLA-LAEHVVPAVRAVNVAEEDLQDVVRELGLKQGFDV 236 M A A GA V++ D+ ++LA A++ PAV V+V E L DVVR+ G DV Sbjct: 180 MTALAALAGGAARVILADVVAEKLAHFADN--PAVITVDVTRETLTDVVRQATDGWGADV 237 Query: 237 GLEMSGSQAALDQMVEALVMGGKIALLGIPPGKSPVDWSRIVFKAITIKGVYGREMFETW 296 E SG +++ + GG L+G+PP +D + K + ++ V+ + Sbjct: 238 VFEASGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVF--RYANIF 295 Query: 297 YKMIAMLQNG-LDVSRVITHRFDVEDFAEGFAAMKSGRSGKVVLR 340 + +A++ +G +DV I+ +F F SGR V ++ Sbjct: 296 PRALALISSGMIDVKPFISRKFPFSQSIRAFEEAASGRPQDVKIQ 340 Lambda K H 0.320 0.139 0.421 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: 266 Number of extensions: 18 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: 345 Length adjustment: 29 Effective length of query: 313 Effective length of database: 316 Effective search space: 98908 Effective search space used: 98908 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 (21.8 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