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_011911952.1 PST_RS03775 succinate-semialdehyde dehydrogenase I
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000013785.1:WP_011911952.1 Length = 488 Score = 222 bits (565), Expect = 3e-62 Identities = 151/456 (33%), Positives = 228/456 (50%), Gaps = 24/456 (5%) Query: 14 ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQ 73 AD+G ++FNP+TGE + VP R ++AI+AA+AA PAWR +RA L R+ + Sbjct: 24 ADSGARTEIFNPATGELIGVVPNMGRGETRRAIEAAQAAQPAWRALTAKERAARLRRWYE 83 Query: 74 LLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGPNIDAW 133 L+ N+E + ++++ E GK + +A GE V YA + E E R G I A Sbjct: 84 LMLENQEDLARIMTAEQGKPLAEARGE-------VAYAASFLEWFAEEGKRLYGDVIPAH 136 Query: 134 S-------DFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAE 186 + +P+GV A ITP+NFP+ + A+A G +LKP+ + P S L +A Sbjct: 137 AGDKRILVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTPFSALALAA 196 Query: 187 LFHEAGLPKGVLNVVHGDKGA---VDA-LIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242 L AG+P G+ +V+ D V A L E P V+ LSF GST + + + K+ Sbjct: 197 LAERAGIPAGLFSVITADAATSREVGAELCEHPVVRKLSFTGSTAVGIKLMQQCAPTLKK 256 Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302 + G ++ DADLD V M + Y + G+ C+ + + V D I DA V K Sbjct: 257 LSLELGGNAPFIVFDDADLDATVEGAMISKYRNAGQTCVCAN-RIYVQDGIYDAFVDKFS 315 Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362 + LK+G G G+ GPL+ AA KV ++ + +GA L+ G+ + + G+ Sbjct: 316 AAVARLKVGNGAEEGVTTGPLIDAAAVAKVQRHLQDALDKGATLLAGGKPHALGGN---- 371 Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422 F TL VT EM + +EE FGP+ + R E ++ ND E+G + RD Sbjct: 372 FFEPTLVGGVTAEMDVAREETFGPLAPLFRFRDEAEVIRQANDTEFGLAAYFYARDLSRV 431 Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458 + +E GMVG+N + + FGG K S G Sbjct: 432 FRVAEALEYGMVGINTGV-ISTEVAPFGGMKASGLG 466 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: 609 Number of extensions: 33 Number of successful extensions: 5 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: 488 Length adjustment: 34 Effective length of query: 464 Effective length of database: 454 Effective search space: 210656 Effective search space used: 210656 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 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