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 WP_029133105.1 A3GO_RS0108930 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000428045.1:WP_029133105.1 Length = 497 Score = 724 bits (1868), Expect = 0.0 Identities = 346/496 (69%), Positives = 405/496 (81%) Query: 1 MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60 M I H I GE++ D RT ++NP+TGE R+V LA R T+++AI AA+AAFPAWR TP Sbjct: 1 MNTIGHFINGEIVNDDQRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETP 60 Query: 61 PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120 P KRAQV+FR+KQLLE + E I LI++EHGK ++DA GEL RGIE VEYA APE+LKG Sbjct: 61 PLKRAQVMFRYKQLLEQHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKG 120 Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180 EYS++VGP ID+WS+FQP+GVV GITPFNFP MVP+WM+P+AI CGNTFILKPSERDPS+ Sbjct: 121 EYSKSVGPAIDSWSEFQPLGVVVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSA 180 Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 L IAEL +AGLP GV N+V+GDK AVD L+ P V+A SFVGST +AEYIY GT G Sbjct: 181 ALRIAELLQQAGLPDGVFNLVNGDKEAVDTLLNDPRVQAASFVGSTMVAEYIYHTGTAAG 240 Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300 KRVQALGGAKNHAV+MPDADLDNAV+ALMGAAYGSCGERCMAISV VCVGD +ADA+V Sbjct: 241 KRVQALGGAKNHAVVMPDADLDNAVNALMGAAYGSCGERCMAISVVVCVGDTVADAVVGG 300 Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360 L ++ LK+G G G +MGPLVT KV GY+D G+ +GAELVVDGRG +V GH Sbjct: 301 LAEKLAHLKVGPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVVDGRGQRVEGHAE 360 Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 GFFLGG LFDRVTPEM+IY++EIFGPVLC+VRV +L++AM LI++HEYGNGTCIFTRDGE Sbjct: 361 GFFLGGCLFDRVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTRDGE 420 Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480 AAR F D I VGMVGVN+PLPVPVAYHSFGGWKRSLFGDLHAYGPD VRFYT+RK ITQR Sbjct: 421 AARFFSDHIRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTITQR 480 Query: 481 WPQRKSHEAAQFAFPS 496 WP E + +AFP+ Sbjct: 481 WPSASVREGSSYAFPT 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: 818 Number of extensions: 25 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 Apr 09 2024. 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