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_012566781.1 RC1_RS07630 succinate-semialdehyde dehydrogenase I
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000016185.1:WP_012566781.1 Length = 508 Score = 232 bits (591), Expect = 3e-65 Identities = 146/446 (32%), Positives = 228/446 (51%), Gaps = 7/446 (1%) Query: 14 ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQ 73 AD+G+T V NP+ G + VP ++AI AA+ A+PAWR +RAQVL R+ + Sbjct: 45 ADSGKTIAVTNPADGSTLGSVPAMGAAEARRAIAAAERAWPAWRTKTAKERAQVLRRWYE 104 Query: 74 LLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGPNIDAW 133 L+ A++E + ++++ E GK + ++ GE+ +E+ + + G+ P Sbjct: 105 LMLAHQEDLARIMTAEQGKPLAESRGEIVYAANFLEWFAEEAKRVYGDVIPTHRPGSRIV 164 Query: 134 SDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAGL 193 +P+GV A ITP+NFPA + A+A G ++KP+ P S L +A L AG+ Sbjct: 165 VVKEPVGVTAAITPWNFPAAMITRKAGPALAAGCPMVVKPASYTPFSALAMAVLAERAGV 224 Query: 194 PKGVLNVVHGDKGAVDA-LIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAKNH 252 P GVL+VV G GA+ P V+ LSF GST I + + ++ K++ G Sbjct: 225 PPGVLSVVTGSAGAIGGEFTSNPAVRKLSFTGSTEIGKTLMAQCAGTVKKLSLELGGNAP 284 Query: 253 AVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKIGA 312 ++ DADLD AV + + Y + G+ C+ + + V D + DA +L ++GLK+ Sbjct: 285 FIVFDDADLDAAVQGAIASKYRNTGQTCVCAN-RLLVQDGVYDAFAARLADAVRGLKVAN 343 Query: 313 GTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFDRV 372 G G GPL+ AA +KV +I V++GA +V GR + + G F T+ V Sbjct: 344 GLEDGATQGPLIDMAAVEKVEEHIRDAVSKGARIVTGGRRHALGGS----FFEPTVLADV 399 Query: 373 TPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVG 432 TP M + +EE FGPV + R EA+ L N EYG + RD + +E G Sbjct: 400 TPAMAVAREETFGPVAPLFRFKDEAEAIHLANATEYGLAAYFYARDLGRVWRVAEALEYG 459 Query: 433 MVGVNVPLPVPVAYHSFGGWKRSLFG 458 ++G+N + + FGG K S G Sbjct: 460 IIGINEGI-ISTEVAPFGGMKESGLG 484 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: 616 Number of extensions: 27 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: 508 Length adjustment: 34 Effective length of query: 464 Effective length of database: 474 Effective search space: 219936 Effective search space used: 219936 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