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_041098592.1 SUTH_RS08615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000828635.1:WP_041098592.1 Length = 480 Score = 250 bits (638), Expect = 9e-71 Identities = 160/453 (35%), Positives = 242/453 (53%), Gaps = 7/453 (1%) Query: 7 LIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQ 66 LI GE +A TG T D+ NP+TGEAV VP ++AIDAA AAF WR A+RA+ Sbjct: 12 LINGEWLAATGATLDIRNPATGEAVGSVPGFGAAETRRAIDAAHAAFHPWRAKTAAERAK 71 Query: 67 VLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNV 126 +L R+ +L+ N+E + +L+++E GK + +A GE+ +E+ + G+ + Sbjct: 72 ILRRWFELMMENQEDLARLMTQEQGKPLAEARGEIAYAASFIEWFAEEARRIYGDVIPSP 131 Query: 127 GPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAE 186 + QP+GV A ITP+NFPA + A+A G T ++KP+E+ P S L +A Sbjct: 132 LADRRLIVLKQPVGVCAAITPWNFPAAMITRKVAPALAAGCTMVVKPAEQTPLSALALAW 191 Query: 187 LFHEAGLPKGVLNVVHGDKGAVDA-LIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQA 245 L +AGLP GVLNVV G+ A+ L P+V LSF GST I + + K++ Sbjct: 192 LGQQAGLPPGVLNVVTGEPVAIGGELTSNPKVLKLSFTGSTEIGRLLMGQCAPTIKKMSL 251 Query: 246 LGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQI 305 G ++ DADLD AV+ M + Y + G+ C+ + V + + DA Q+L + Sbjct: 252 ELGGNAPFIVFDDADLDAAVAGAMLSKYRNTGQTCVCTN-RFLVQEGVHDAFAQRLAAAV 310 Query: 306 KGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLG 365 GLK+G G G+ GPL+ GA KV + +A+GA ++ G+ + + G F Sbjct: 311 AGLKVGYGLEEGVTQGPLIDGAGLAKVEELLADALAKGARVLCGGKRHA----KGGTFFE 366 Query: 366 GTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLF 425 T+ TP M + +EEIFGPV I +A+++ ND E+G F+RD A Sbjct: 367 PTVLAGATPAMRLAREEIFGPVAPIFSFKDEADAIRMANDTEFGLAAYFFSRDIARAWRV 426 Query: 426 CDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458 + ++ GMVG+N + + FGG K+S G Sbjct: 427 GEALDYGMVGINSGM-ISNEVAPFGGVKQSGLG 458 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: 602 Number of extensions: 32 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: 480 Length adjustment: 34 Effective length of query: 464 Effective length of database: 446 Effective search space: 206944 Effective search space used: 206944 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