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_011771045.1 PING_RS14365 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000015285.1:WP_011771045.1 Length = 481 Score = 221 bits (564), Expect = 3e-62 Identities = 143/479 (29%), Positives = 244/479 (50%), Gaps = 12/479 (2%) Query: 6 HLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRA 65 ++ G ++ T T +V+NP+ E + V A E + AI+AA AF WR P +RA Sbjct: 12 YINGQFILTATKTTFNVYNPANNECLASVENAGEEEVVNAINAADQAFALWRTVAPRERA 71 Query: 66 QVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRN 125 ++L ++ N+E I LIS E GKT+ ++ GE+ E + + + G+ SR+ Sbjct: 72 EILRSCYNIMIKNKENIANLISLEEGKTLSESLGEVNYAAEFFRWFSEEAVRINGDLSRS 131 Query: 126 VGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIA 185 N + +P+G+ ITP+NFPA + A+A G + I+KPSE P + L +A Sbjct: 132 PSGNNNILVTNEPVGICYLITPWNFPAAMMTRKIAPALAAGCSVIVKPSEETPLTALYLA 191 Query: 186 ELFHEAGLPKGVLNVVHGDK--GAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRV 243 +LF EAG+PKG++NV+ ++ +A+ + ++ +SF GST I ++ S+ +K+ Sbjct: 192 QLFSEAGVPKGLINVLPSNRPEELSEAIFKDNRIRKISFTGSTNIGSHLLSKASKKVVNC 251 Query: 244 QALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVP 303 G +++ DADLD A+ + M A + GE C+A + V +A + +KL Sbjct: 252 SMELGGNAPFIVLDDADLDVAIDSAMIAKMRNAGESCIAAN-RFYVHQSLAASFTEKLTK 310 Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363 ++ LK+G G D+GPL+ A KV G + + +GA+L G + + + Sbjct: 311 KMAVLKVGNGLDSTTDVGPLINRKAVIKVDGLVQEAIKKGAKLHCGGGLIE----SDSCY 366 Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423 T+ + + I+ +EIFGPV I + ++ + N+ ++G I + D + A Sbjct: 367 YSPTVLSNIPKDADIFSQEIFGPVAAISTFDDIDSVISSANNTDFGLAAYIISADIKKAL 426 Query: 424 LFCDEIEVGMVGVNVP-LPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481 +E G++G+N + P A FGG K+S G G DG+ + ++K I W Sbjct: 427 RVASLLEAGVIGINQGFISDPAA--PFGGVKQSGLG--REGGGDGIWEFIEKKYIAVDW 481 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: 527 Number of extensions: 24 Number of successful extensions: 4 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: 481 Length adjustment: 34 Effective length of query: 464 Effective length of database: 447 Effective search space: 207408 Effective search space used: 207408 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