Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_106712403.1 CU102_RS17560 L-idonate 5-dehydrogenase
Query= reanno::Phaeo:GFF3379 (342 letters) >NCBI__GCF_003010955.1:WP_106712403.1 Length = 348 Score = 140 bits (352), Expect = 6e-38 Identities = 102/339 (30%), Positives = 166/339 (48%), Gaps = 16/339 (4%) Query: 11 EGLWMVQAPVPEIGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPMITGHEFAGEIV 70 E L +V + E+ P+ V ++ GICG+DIH + V P+I GHE AGEIV Sbjct: 14 EDLRVVDVELGELEPNMVRVRFGAGGICGSDIHYFRHARTGDFVVTSPLILGHEVAGEIV 73 Query: 71 EIGRNVTDLAVGQRCSGEGHLIQTDSRQSRAGKFHLDP-----GTRGIGVNEQGAFAQYL 125 E+G NVT LAVG+R + G+ +L G+ + QG FA Sbjct: 74 EVGSNVTGLAVGERVAVNPSRWCERCVYCHEGRANLCENIYFMGSASKTPHMQGGFASLF 133 Query: 126 KLPAFNVVPLPEDIPDEIGAILDPLGNAVHTA-LSFDLLGEDVLITGAGPIGVMAAAVAR 184 A V +P D+P + A+ +PL +H + + G ++ GAGPIG++ + Sbjct: 134 DATAAQCVRVPADLPFQAAALAEPLAVCLHAVRRAGHVKGFSTIVFGAGPIGLLTMLALK 193 Query: 185 HAGARHVVITDINPDRLALAEHVVPAVRAVNVAEEDLQDVVRELGLKQGFDVGLEMSGSQ 244 HA A V + D+ L AE + A + V++++ +D + +L FD+ E+SG+ Sbjct: 194 HADAGSVTMVDVAAAPLKFAEE-LGADQIVDLSQG--EDQLAQLATVSPFDIAFEISGTA 250 Query: 245 AALDQMVEALVMGGKIALLG-IPPGKSPVDWSRIVFKAITIKGV--YGREMFETWYKMIA 301 A L + + GG + +G + G PV + ++ K + + G +G E FE + Sbjct: 251 AGLASAIRTVRRGGTVVQVGNLAGGTIPVPANAVMAKELDLIGTFRFGEEFFEA---VEL 307 Query: 302 MLQNGLDVSRVITHRFDVEDFAEGF-AAMKSGRSGKVVL 339 +++ +DV R++T + + D E F A+ RS KVVL Sbjct: 308 IVEGKIDVLRLVTSEYKLADAPEAFRTALDRSRSVKVVL 346 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: 295 Number of extensions: 15 Number of successful extensions: 4 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: 348 Length adjustment: 29 Effective length of query: 313 Effective length of database: 319 Effective search space: 99847 Effective search space used: 99847 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 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