Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_086509055.1 BZY95_RS05955 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_002151265.1:WP_086509055.1 Length = 516 Score = 337 bits (865), Expect = 5e-97 Identities = 190/471 (40%), Positives = 264/471 (56%), Gaps = 10/471 (2%) Query: 52 KTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADL 111 +T ++P+TGE + + V++AV +A A Q W + AS RGR +N Sbjct: 41 ETITLIDPATGEALLDYRDAGPALVERAVSSASRAQQA---WMALTASERGRRMNAAVRG 97 Query: 112 IERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYT 171 +E LA LE++ GKP + ++ V + YYAGW DK HG+ IP+ +Y Sbjct: 98 LEGHEEALAQLESVVAGKP-IRDCRGEVGKVREMFDYYAGWCDKQHGEVIPVPTSHLNYV 156 Query: 172 RHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFP 231 RH P GV GQI PWN P+ AW+L PA+A GN V+K +E TP T++ +A L++ G P Sbjct: 157 RHVPYGVVGQITPWNAPMFTCAWQLAPAIAAGNGAVLKPSELTPFTSVVIARLLERGGLP 216 Query: 232 PGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSP 291 G+VNIV G GP+ GAA+ E + K+ F GS + GR+I AG+ L LELGGKS Sbjct: 217 KGLVNIVNGLGPSTGAALTGSEGISKLVFVGSPQSGRLI-AEAGARRLVPSVLELGGKSA 275 Query: 292 NIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNP 351 NI+ +DA +D AV A A+F GQ C AGSR VQ +++ E ER A VG P Sbjct: 276 NIVFADASLDAAVAGAQAAIFAAAGQSCVAGSRLLVQREVFAEVTERLARAAAGIEVGLP 335 Query: 352 FDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD-----RGYFIQPTVFGDV 406 D T GP + Q+ + I GA+++ GG A RGYF+ PTV DV Sbjct: 336 GDEATRMGPLQNARQYAHVTRMIEDAVAAGARVIVGGSRPAGLPEEARGYFLAPTVLVDV 395 Query: 407 QDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAG 466 M IA+EE+FGPV+ + F + V AN + +GLA AV+T+D +A+ ++ L+AG Sbjct: 396 TPEMEIAREEVFGPVLVAMPFDDEADAVRLANATRFGLAGAVWTQDPARAHRVAAQLRAG 455 Query: 467 TVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQKNS 517 TVW+N Y SPFGG+ SG GR G GL+ YT ++V V+ + S Sbjct: 456 TVWINGYKAISVMSPFGGFGDSGFGRSSGLDGLREYTLPQSVWVETASEAS 506 Lambda K H 0.319 0.136 0.409 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: 642 Number of extensions: 28 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: 517 Length of database: 516 Length adjustment: 35 Effective length of query: 482 Effective length of database: 481 Effective search space: 231842 Effective search space used: 231842 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 (21.8 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