Align Aldehyde dehydrogenase family 7 member B4; Antiquitin-1; Turgor-responsive ALDH; EC 1.2.1.3 (characterized)
to candidate WP_028584713.1 G494_RS0111845 aldehyde dehydrogenase family protein
Query= SwissProt::Q9SYG7 (508 letters) >NCBI__GCF_000429965.1:WP_028584713.1 Length = 510 Score = 497 bits (1279), Expect = e-145 Identities = 255/507 (50%), Positives = 345/507 (68%), Gaps = 8/507 (1%) Query: 9 EFLSEIGLTSHNLGSYVAGKWQA--NGPLVSTLNPANNQPIAQVVEASLEDYEQGLKACE 66 +F+ ++G+ N G W + + + +P + + IA V E+ EQ L + Sbjct: 2 DFIHQLGIRKLNSGVSTGTSWLSPTREKRLKSRSPIDGKVIASVRCGGAEELEQILATAQ 61 Query: 67 EAAKIWMQVTAPKRGDIVRQIGDALRSKLDYLGRLLSLEMGKILAEGIGEVQEVIDMCDF 126 E+ +W QV P+RGDIVRQIG LR + + LGRL+SLEMGK L EG GEVQE+ID+CDF Sbjct: 62 ESCALWQQVPPPQRGDIVRQIGLELREQKEALGRLVSLEMGKSLQEGYGEVQEMIDICDF 121 Query: 127 AVGLSRQLNGSVIPSERPNHMMLEMWNPLGIVGVITAFNFPCAVLGWNACIALVCGNCVV 186 AVG SR L+G+ + SERP H + + ++PLG+VG++TAFNFP AV WNA I+ VCGN + Sbjct: 122 AVGQSRLLSGATLQSERPLHRIYDQYHPLGLVGIVTAFNFPVAVWSWNAMISAVCGNVNI 181 Query: 187 WKGAPTTPLITIAMTKLVAEVLEKNNLPGAIFTAMCG-GAEIGEAIAKDTRIPLVSFTGS 245 WK + PL IA+ L+ VL N LP IF+ + G G +G+A+ +D RIPL+SFTGS Sbjct: 182 WKPSSLVPLTAIAVQHLIGRVLRSNQLPEGIFSLVIGSGRSVGQAMLQDPRIPLISFTGS 241 Query: 246 SRVGSMVQQTVNARSGKTLLELSGNNAIIVMDDADIQLAARSVLFAAVGTAGQRCTTCRR 305 G QTV AR GK++LEL GNNAII+ AD++LA +V+F AVGTAGQRCTT RR Sbjct: 242 VATGRQAAQTVAARLGKSILELGGNNAIIITPQADLKLAIPAVVFGAVGTAGQRCTTTRR 301 Query: 306 LLLHESVYDKVLEQLLTSYKQVKIGNPLEKGTLLGPLHTPESKKNFEKGIEVIKSQGGKI 365 L++H+ VY +V E L+T+Y+ ++IG+PL+ +GPL E+ +E+ + I +QGG+I Sbjct: 302 LIVHKKVYKQVKEALITAYQSLRIGSPLDPVNHVGPLVNQEAVAAYEQAVTAITAQGGRI 361 Query: 366 LTGGKAVEGEGN----FVEPTIIEISADAAVVKEELFAPVLYVLKFK-SFGEAVAINNSV 420 + GGK + G+G +V PT++E +V+EE FAP+LY+LK+K + +A+AI N V Sbjct: 362 IFGGKVLSGKGYASGCYVMPTLVEAEPSMPLVREETFAPILYLLKYKGALEQAIAIQNGV 421 Query: 421 PQGLSSSIFTRNPENIFRWIGPLGSDCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSD 480 QGLSS+IFT ++ GSDCGI NVN+ T+G+EIGGAFGGEK TGGGREAGSD Sbjct: 422 SQGLSSAIFTTGLAEAETFLSNQGSDCGIANVNLGTSGSEIGGAFGGEKETGGGREAGSD 481 Query: 481 SWKQYMRRSTCTINYGNELPLAQGINF 507 +WK YMRR T TIN+G LPLAQGI F Sbjct: 482 AWKAYMRRQTVTINHGTALPLAQGITF 508 Lambda K H 0.317 0.135 0.398 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: 694 Number of extensions: 31 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: 508 Length of database: 510 Length adjustment: 34 Effective length of query: 474 Effective length of database: 476 Effective search space: 225624 Effective search space used: 225624 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 (21.6 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