Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__WCS417:GFF3484 Length = 486 Score = 382 bits (982), Expect = e-110 Identities = 200/470 (42%), Positives = 287/470 (61%), Gaps = 13/470 (2%) Query: 50 SRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLA 109 S+ TF NP+TGE I +VA G E+V AV AA+ AF W A R RL+ +L Sbjct: 13 SKDTFINYNPATGEAIGEVASGGAEEVALAVAAAKEAFP---KWANTPAKERARLMRKLG 69 Query: 110 DLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFS 169 +LIE++ +LA LETLD G P + V + ++A + G + P+D + Sbjct: 70 ELIEQNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHSYPVDDQMLN 129 Query: 170 YTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG 229 YT ++PVGVCG + PWN P + WK P LA GN V+K++E +PLTA + L EAG Sbjct: 130 YTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEAG 189 Query: 230 FPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGK 289 P GV+N++ G+G TAG A+ H DV ++FTG T G+ I AG LK+ ++ELGGK Sbjct: 190 IPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---LKKYSMELGGK 246 Query: 290 SPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVG 349 SP +I DAD++ A++ A F +F G+ C AGSR F+QE +Y +FV ARAK +VG Sbjct: 247 SPVLIFEDADLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVG 306 Query: 350 NPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG-------GIAADRGYFIQPTV 402 +P D KT+ G + + + K+ GYI G +EGA LL GG +G FIQPTV Sbjct: 307 DPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAHLSKGQFIQPTV 366 Query: 403 FGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQA 462 F DV + M IA+EEIFGPV+ ++ FK E + AN++ YGLA+ ++T+D+ KA+ L++ Sbjct: 367 FADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDIGKAHRLARG 426 Query: 463 LQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 ++AG V++N +V + PFGG K SG+GRE G+Y + + E+K V + + Sbjct: 427 IEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 476 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: 617 Number of extensions: 25 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: 486 Length adjustment: 34 Effective length of query: 483 Effective length of database: 452 Effective search space: 218316 Effective search space used: 218316 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 17 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