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 AO353_06080 AO353_06080 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__pseudo3_N2E3:AO353_06080 Length = 497 Score = 903 bits (2334), Expect = 0.0 Identities = 442/496 (89%), Positives = 465/496 (93%) Query: 1 MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60 M+LI HLI GEL+ D RTADVFNPSTG+ + KVPLA RET+Q+AID+AKAAFPAWRNTP Sbjct: 1 MSLIPHLINGELVTDNARTADVFNPSTGQPIHKVPLASRETIQKAIDSAKAAFPAWRNTP 60 Query: 61 PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120 PAKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG Sbjct: 61 PAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120 Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180 EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180 Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 TLLIA+L EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGTKRG Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRG 240 Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADALV K Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVTK 300 Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360 LVPQIK LKIGAGTSCGLDMGPLV+G ARDKV+GYI+ GV+ GA L+VDGRG VAGHE Sbjct: 301 LVPQIKALKIGAGTSCGLDMGPLVSGQARDKVSGYIEDGVSAGASLIVDGRGLSVAGHEE 360 Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 GFFLGG LFD VTPEM IYKEEIFGPVLCIVRVNSLE AMQLINDHEYGNGTCIFTRDGE Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCIVRVNSLEAAMQLINDHEYGNGTCIFTRDGE 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: 903 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:
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