Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_01155 H281DRAFT_01155 2,5-dioxopentanoate dehydrogenase (NAD+)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >FitnessBrowser__Burk376:H281DRAFT_01155 Length = 481 Score = 255 bits (651), Expect = 3e-72 Identities = 157/475 (33%), Positives = 246/475 (51%), Gaps = 9/475 (1%) Query: 13 KLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGA 72 +LLI+GEW ++ + + D+VNPAT QV+ KV A A++D A+ AA R F+ W+ P Sbjct: 10 RLLINGEWCDAASGKTIDVVNPATGQVIGKVAHAGIADLDRALEAAQRGFEAWRKVPAHE 69 Query: 73 RMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFA 132 R +M K AL+RE + I +++ EQGK A+A+ ++ +++E G G Sbjct: 70 RAAVMRKAAALVRERASDIGRLMTQEQGKPFAEAKIEVLAAADIIEWFADEGRRLYGRVV 129 Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192 + L++PIG A TP+NFP + A+A G +F++K E+ P S Sbjct: 130 PSRNLAAQQLVLKEPIGPVAAFTPWNFPVNQIVRKLSAALASGCSFLVKAPEETPASPAG 189 Query: 193 LVELAIEAGIPPGVLNVVHGG-KDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 251 L++ +EAG+P G + +V G ++ L H I+ V+F GST VG + LAG H KR Sbjct: 190 LLQAFVEAGVPAGTVGLVFGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGAHMKR 249 Query: 252 VQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMA-TSVVVLVGAAKQWLPDLKA 310 +G +V DA+ A+ A GA F AGQ C++ T +V +++ L Sbjct: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIREEFAAALVK 309 Query: 311 LAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNF 370 A+ LK+ G GT +GP+ + R + +++ K GAK+E G + +GNF Sbjct: 310 HAEGLKLGDGLAEGTTLGPLANARRLTAMSKVLDDARKTGAKIETGGERVG----SEGNF 365 Query: 371 VGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAAR 430 PT+ + V+ E ++ E FGP+ + D L++AIA N PFG FT+S + Sbjct: 366 FAPTVLTNVSLEADVFNNEPFGPIAAIRGFDKLEEAIAEANRLPFGLAGYAFTKSFSNVH 425 Query: 431 KFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 485 +++VG + IN P P P F G + S G G G + ++ Y TK+VT Sbjct: 426 LLSQQLEVGMLWINQP-ATPTPEMPFGGVKDSGYGSEG--GPEAMEAYLVTKSVT 477 Lambda K H 0.319 0.135 0.397 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: 572 Number of extensions: 28 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: 505 Length of database: 481 Length adjustment: 34 Effective length of query: 471 Effective length of database: 447 Effective search space: 210537 Effective search space used: 210537 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 (21.7 bits) S2: 52 (24.6 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