Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_011912900.1 PST_RS08835 betaine-aldehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >NCBI__GCF_000013785.1:WP_011912900.1 Length = 490 Score = 249 bits (637), Expect = 1e-70 Identities = 170/480 (35%), Positives = 249/480 (51%), Gaps = 18/480 (3%) Query: 8 FIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAATNPQRRA 67 +I G VD +S + E +P G+V A VA A A +L A+ +A+ Q WAA RA Sbjct: 10 YIHGAYVDASSNQTFESINPANGEVLAEVAEAGAADLERAVESAEQGQRIWAALTGIERA 69 Query: 68 RVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYTQ 126 R+M LL DELA L + + GK +++++ DI G +V+E+ G+ ++GE Sbjct: 70 RIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIITGADVLEYYAGLAPAIEGEQIP 129 Query: 127 GAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPVRL 186 VY+ R+PLGVVAGI +N+P I +W PA+A GNA I KPSE P +RL Sbjct: 130 LRDSSF-VYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTPLSALRL 188 Query: 187 AELMIEAGLPPGVLNVVHGDKDCVEAIL-DHPDIKAVSFVGSSDIAQSVF-QRAGAAGKR 244 AE+ EAGLP GV NV+ G V A++ +HP I VSF G + V AG++ K Sbjct: 189 AEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAAGSSLKD 248 Query: 245 VQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCM-ALPVVVPVGEKTATALREKL 303 V G K+ +V DADLD+A + A + S+G+ C V +P G K + KL Sbjct: 249 VTMELGGKSPLIVCEDADLDRAADIAVMANFFSSGQVCTNGTRVFIPAGLK--ASFEAKL 306 Query: 304 VAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHEEG 363 + + +R+G ++GP+VS AH ++ YI G GA ++ G + + G Sbjct: 307 LERVQRVRLGDPQQEATNFGPLVSFAHMDKVLDYIAQGKAAGARILCGGERVTEGEYARG 366 Query: 364 FFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNGDA 423 FV PT+F +EIFGPVL ++ + +E I A+ +YG + T + Sbjct: 367 AFVAPTIFSDCSDDMSIVREEIFGPVLSLLEYQGEDEAIRRANDTEYGLAAGVVTPDLAR 426 Query: 424 AREFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTV 479 A ++E G+ IN P +PV GG+K+SG G N G+ + YTR K+V Sbjct: 427 AHRIIHRLEAGICWINTWGESPAQMPV-----GGYKQSGIGREN--GIASLAHYTRVKSV 479 Lambda K H 0.320 0.137 0.409 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: 587 Number of extensions: 30 Number of successful extensions: 7 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: 500 Length of database: 490 Length adjustment: 34 Effective length of query: 466 Effective length of database: 456 Effective search space: 212496 Effective search space used: 212496 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: 52 (24.6 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