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_011840207.1 RSPH17029_RS00810 aldehyde dehydrogenase family protein
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000015985.1:WP_011840207.1 Length = 486 Score = 209 bits (532), Expect = 2e-58 Identities = 165/488 (33%), Positives = 241/488 (49%), Gaps = 20/488 (4%) Query: 6 HLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRA 65 ++ GG R +V +PST EA + L D+ A+ AAKAAF W TPPA+R Sbjct: 8 YINGGWTAPAKARDCEVIDPSTEEACAVISLGDQADTDAAVAAAKAAFEGWAATPPAERL 67 Query: 66 QVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGI--ENVEYATAAPEILKGEYS 123 +++ EA +E + + IS E G I+ A + + A EI E+ Sbjct: 68 RLVKGILAQYEARKEEMAQAISLEMGAPIDLARNSQAPCLPWHLTNFLKAFEEI---EWV 124 Query: 124 RNVGPNIDAWSD---FQPIGVVAGITPFNFPA-MVPLWMYPLAIACGNTFILKPSERDPS 179 R +GP+ A +D +PIGVV ITP+N+P V L + P A+ G T +LKPSE P Sbjct: 125 RPLGPH--APNDRIALEPIGVVGLITPWNWPMNQVTLKVIP-ALLAGCTCVLKPSEEAPL 181 Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEA-PEVKALSFVGSTPIAEYIYSEGTK 238 S+LL AE H+AGLP GV N+V+GD V + + P+V+ +SF GST I + Sbjct: 182 SSLLFAEFVHDAGLPAGVFNLVNGDGAGVGTQLSSHPDVEMISFTGSTRAGRAISKAAAE 241 Query: 239 RGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALV 298 KRV G K ++ DAD + AV + + + G+ C A + V D V Sbjct: 242 SLKRVTLELGGKGANLIFADAD-ERAVERGVKHCFNNSGQSCNA-PTRMLVERPFYDRAV 299 Query: 299 QKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGH 358 + ++ + G +GP+V +++ YI G+ +GA LV G G + G Sbjct: 300 EIAAEVAAKTRVASAHEEGPHIGPVVNKRQFEQIQSYIQKGIDEGARLVAGGLG-RPDGL 358 Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418 GFF+ T+F VTP MTI +EEIFGPVL I+ + EEA+++ ND YG + + D Sbjct: 359 NRGFFVRPTVFADVTPGMTIEREEIFGPVLSILPFETEEEAVRIANDTPYGLTNYVQSED 418 Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478 G + GMV +N A FGG K S G G G+ + + KAI+ Sbjct: 419 GARRNRLARRLRSGMVEMNGKSRGAGA--PFGGVKAS--GRAREGGVWGIEEFLEVKAIS 474 Query: 479 QRWPQRKS 486 P+ ++ Sbjct: 475 GWDPEAEA 482 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: 540 Number of extensions: 24 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 498 Length of database: 486 Length adjustment: 34 Effective length of query: 464 Effective length of database: 452 Effective search space: 209728 Effective search space used: 209728 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 10 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