Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase
Query= BRENDA::Q93YB2 (503 letters) >FitnessBrowser__azobra:AZOBR_RS26825 Length = 494 Score = 299 bits (765), Expect = 2e-85 Identities = 183/482 (37%), Positives = 268/482 (55%), Gaps = 16/482 (3%) Query: 10 LFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATA 69 L I G+ + K V+NPAT ++I + DVD AV AA A +GA WA Sbjct: 18 LLIGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAA----QGA-WARL 72 Query: 70 SGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPL-DEAAWDIDDVAGCFEYYADLAEKL 128 S R R L ++ E+ +L +++ GK + E+ + VA +Y LA +L Sbjct: 73 SARERGRLLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASEL 132 Query: 129 DARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSE 188 + P M TF REPIGVVG I PWN P+ + K+APAL AG A I+K +E Sbjct: 133 KG-ETVPFHPKMLTFTQ---REPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAE 188 Query: 189 LASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMT 248 A L L + ++ ++ LPPGVLNIL+G GP GAPL THP V KV FTGS TG I Sbjct: 189 EAPLAALRVIQVMNQL-LPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISH 247 Query: 249 AAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGC-FWTNGQICSATSRLILHESIA 307 AA + PV+LELGGKSP++V D DLDKA + A+ G F GQ C+A+SR+ +HES+ Sbjct: 248 LAADKLIPVTLELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLH 307 Query: 308 TEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGS--- 364 F++++ + + + DPL+E +G ++S Q+E++ +++ ++ I S Sbjct: 308 DAFIDKLKAKVDAMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALP 367 Query: 365 RPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAA 424 E L +G F++P + T + + ++ REE+FGPV CV F E+A+ +AND+ +GL A Sbjct: 368 TDERLARGLFVQPVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAAT 427 Query: 425 VISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELG-EWGLDNYLSVK 483 + + DL T+ +AG V VN + +GG K+SG G+E E LD++ K Sbjct: 428 IWTRDLRTALDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHKK 487 Query: 484 QV 485 V Sbjct: 488 TV 489 Lambda K H 0.318 0.135 0.416 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: 534 Number of extensions: 27 Number of successful extensions: 6 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: 503 Length of database: 494 Length adjustment: 34 Effective length of query: 469 Effective length of database: 460 Effective search space: 215740 Effective search space used: 215740 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 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