Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_052591230.1 VV02_RS09595 aldehyde dehydrogenase
Query= BRENDA::Q4F895 (507 letters) >NCBI__GCF_001190945.1:WP_052591230.1 Length = 507 Score = 772 bits (1994), Expect = 0.0 Identities = 374/507 (73%), Positives = 430/507 (84%) Query: 1 MTVYARPGTADAIMSFQSRYDNWIGNEWVAPVKGQYFENPTPVTGQNFCDVARSTAEDIE 60 MTVY RPG++ + ++ + +Y ++IG E+VAP KG+YFEN P TG+ F V R TAEDIE Sbjct: 1 MTVYERPGSSGSKIAVEDKYGHYIGGEFVAPKKGEYFENYAPQTGEVFTQVGRGTAEDIE 60 Query: 61 LALDAAHAAAPAWGKTSVAERAIILNKIADRMEENLESIALAESWDNGKPIRETLNADIP 120 ALDAAH AA WG TS AERA +L KIADR+E+NLE +A+ ESWDNGK +RETL AD+P Sbjct: 61 AALDAAHNAADKWGTTSPAERAGVLLKIADRIEKNLEDLAVIESWDNGKAVRETLAADLP 120 Query: 121 LAIDHFRYFAGAIRAQEGSLSEINSDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPAL 180 LA+DHFRYFAGA+RAQEG +SEI+ +T+AYHFHEPLGVVGQIIPWNFPILMA WKLAPAL Sbjct: 121 LAVDHFRYFAGALRAQEGGVSEIDENTIAYHFHEPLGVVGQIIPWNFPILMATWKLAPAL 180 Query: 181 AAGNAIVLKPAEQTPVSILHLIGIIGDLLPAGVLNIVNGFGVEAGKPLASSPRIKKIAFT 240 AAGNA+VLKPAEQTP SIL +I +IGDLLP GVLNIVNGFG EAGKPLAS+ R+ K+AFT Sbjct: 181 AAGNAVVLKPAEQTPWSILKVIELIGDLLPPGVLNIVNGFGTEAGKPLASNKRVAKVAFT 240 Query: 241 GETTTGRLIMQYASQNLIPVTLELGGKSPNIFFSDVLASNDDYQDKALEGFTMFALNQGE 300 GETTTGRLIMQYASQN+IPVTLELGGKSPN+FF DV A D + DKA EGF MFALNQGE Sbjct: 241 GETTTGRLIMQYASQNIIPVTLELGGKSPNVFFEDVAAERDAFYDKAQEGFAMFALNQGE 300 Query: 301 VCTCPSRSLIQEDIFDEFLAMAAIRTKAVRQGDPLDTDTMIGAQASNDQLEKILSYIEIG 360 VCTCPSR+L+Q I+ +F+ A R + ++ G+PLDT+T +GAQASNDQLEKI SY++IG Sbjct: 301 VCTCPSRALVQSSIYSDFMKDAVARVEKIKMGNPLDTETTMGAQASNDQLEKIKSYLDIG 360 Query: 361 KAEGAKVITGGERAELGGDLSGGYYVQPTVFTGNNKMRIFQEEIFGPVVSVTSFKDYDEA 420 K EGAKV+TGGE A+L GDL+GGYYVQPTVF G+N MRIFQEEIFGPVVSVT F D +A Sbjct: 361 KREGAKVLTGGEEAKLEGDLAGGYYVQPTVFEGDNSMRIFQEEIFGPVVSVTPFNDEADA 420 Query: 421 IEIANDTLYGLGAGVWSRDGGVAYRAGRDIQAGRVWTNTYHQYPAHAAFGGYKQSGIGRE 480 ++ ANDTLYGLGAGVWSRDG AYR GR I+AGRVWTN YH YPAHAAFGGYKQSGIGRE Sbjct: 421 LKTANDTLYGLGAGVWSRDGARAYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 480 Query: 481 NHLMMLSHYQQTKNLLVSYAQKAQGFF 507 NH MML HYQQTKNLLVSY+Q AQGFF Sbjct: 481 NHKMMLDHYQQTKNLLVSYSQDAQGFF 507 Lambda K H 0.318 0.135 0.401 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: 831 Number of extensions: 21 Number of successful extensions: 1 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: 507 Length of database: 507 Length adjustment: 34 Effective length of query: 473 Effective length of database: 473 Effective search space: 223729 Effective search space used: 223729 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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