Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO356_07950 AO356_07950 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 AO356_07950 methylmalonate-semialdehyde dehydrogenase Length = 497 Score = 905 bits (2339), Expect = 0.0 Identities = 444/496 (89%), Positives = 466/496 (93%) Query: 1 MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60 M+LI HLI GE ++D+ RTADVFNPSTG+A+ KVPLADR T+QQAIDAAKAAFPAWRNTP Sbjct: 1 MSLIPHLINGERLSDSARTADVFNPSTGQAIHKVPLADRATIQQAIDAAKAAFPAWRNTP 60 Query: 61 PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120 AKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG Sbjct: 61 AAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120 Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180 EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180 Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 TLLIA+L EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGT+RG Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTRRG 240 Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADALV K Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVSK 300 Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360 LVPQIK LKIGAGTSCGLDMGPLVTG RDKV+GYI+ GV GA L+VDGRG VAGHE Sbjct: 301 LVPQIKALKIGAGTSCGLDMGPLVTGQHRDKVSGYIEEGVTAGASLIVDGRGLSVAGHEE 360 Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 GFFLGG LFDRVTPEM IYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE Sbjct: 361 GFFLGGCLFDRVTPEMRIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480 Query: 481 WPQRKSHEAAQFAFPS 496 WPQR SHEA+QFAFPS Sbjct: 481 WPQRASHEASQFAFPS 496 Lambda K H 0.319 0.137 0.411 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: 908 Number of extensions: 17 Number of successful extensions: 1 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: 498 Length of database: 497 Length adjustment: 34 Effective length of query: 464 Effective length of database: 463 Effective search space: 214832 Effective search space used: 214832 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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