Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized)
to candidate WP_075618489.1 GY23_RS06905 aldehyde dehydrogenase family protein
Query= SwissProt::Q41247 (494 letters) >NCBI__GCF_001939075.1:WP_075618489.1 Length = 491 Score = 340 bits (873), Expect = 5e-98 Identities = 187/469 (39%), Positives = 288/469 (61%), Gaps = 17/469 (3%) Query: 22 LGNYVGGKW--LGNGPLVSTLNPANNQVLPIAQVVEASLEDYEIGLKACEEAAKTWMQVP 79 L NY+GGKW G+ VS NPAN + L AQV ++ ED + + A +EA K W VP Sbjct: 3 LNNYIGGKWQEAGDAKYVSVTNPANGEEL--AQVRLSTQEDVNLAVAAAKEAQKKWALVP 60 Query: 80 APKRGDIVRQIGDALRSKLDYLGRLLSLEMGKILAEGIGEVQEVIDMCDFAVGLSRQLNG 139 APKR D + ++G ++ K ++L ++L+ EMGK++ EG GEVQE IDM + G R+L G Sbjct: 61 APKRADYLYEVGRIMKEKKEHLAQVLTKEMGKVIEEGRGEVQEGIDMAFYMAGEGRRLFG 120 Query: 140 SVIPSERPNHMMLEMWNPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLI 199 PSE + + + P+G+VG+IT +NFP A+ W + A+V GN +WK A TP++ Sbjct: 121 ETTPSELADKFAMSVRAPIGVVGLITPWNFPVAIATWKSFPAMVAGNTFLWKPATETPMM 180 Query: 200 TIAMTKLVAEVLEKNHLPGAIFTAMCG-GAEIGEAIAKDTRIPLVSFTGSSKVGLTVQQT 258 M A+V E+ +P + + G GA++G A+ + ++SFTGS++ G +V + Sbjct: 181 AYEM----AKVFEEAGIPDGVANIVFGSGADVGTAMIDHPDVKVISFTGSTETGRSVAER 236 Query: 259 VSARSGKTLLELSGNNAIIVMDDADIQLAARSVLFAAVGTAGQRCTTCRRLLLHESVYDK 318 K LE+ G NA+IVMDDAD+ LA +L++A GTAGQRCT C R+++H+ V ++ Sbjct: 237 GGRNLKKVSLEMGGKNAVIVMDDADLGLAVEGILWSAFGTAGQRCTACSRVIVHKDVKEE 296 Query: 319 VLEQLLTSYKQVKIGDPLEKGTLLGPLHTPESKKNFEKGIEVIKSQGGKVLTGGKAV-EG 377 + +LLTS +Q+ IGD +++ +GP+ ++ + +E+ K++G +L GG+ + +G Sbjct: 297 LESRLLTSMEQLTIGDGMDETVKIGPVINKKALEKIHSYVEIGKNEGATLLVGGEILSDG 356 Query: 378 E---GNFVEPTII-EISSDAAVVKEELFAPVLYALKFKTFEEAVAINNSVPQGLSSSIFT 433 E GN+ PT+ + D+ + +EE+F PV+ ++ + +EA+ +NNSV GLSSSIF+ Sbjct: 357 ELAKGNYYAPTLFTNVDRDSRIAQEEIFGPVVSLIEVSSLDEAIEVNNSVTFGLSSSIFS 416 Query: 434 RSPDNIFKWIGPMGSDCGIVNVNIPTNGAEIGGAFGGEKATGGG-REAG 481 R + +FK D GIV VN T GAEI FGG K TG G R++G Sbjct: 417 RDVNTVFK--AQRDLDTGIVYVNAGTTGAEIHLPFGGTKGTGNGHRDSG 463 Lambda K H 0.316 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: 624 Number of extensions: 29 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: 494 Length of database: 491 Length adjustment: 34 Effective length of query: 460 Effective length of database: 457 Effective search space: 210220 Effective search space used: 210220 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