Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate AZOBR_RS31000 AZOBR_RS31000 aldehyde dehydrogenase
Query= BRENDA::Q9STS1 (503 letters) >FitnessBrowser__azobra:AZOBR_RS31000 Length = 479 Score = 312 bits (799), Expect = 2e-89 Identities = 186/480 (38%), Positives = 262/480 (54%), Gaps = 14/480 (2%) Query: 8 RQLFIGGQWTEPVLRKT-LPVVNPATEDIIGYIPAATSEDVELAVEAARKAFTRNNGKDW 66 + +IGG WTEP T + V+NPATE + G + ED + AV AA AF + Sbjct: 5 QSFYIGGAWTEPAAGATVMEVLNPATEQVSGTVALGGPEDAQRAVAAAHAAFD-----GF 59 Query: 67 ARATGAVRAKYLRAIAAKVIERKSELANLEAIDCGKPLDEAAWDMDDVAGCFEYYADLAE 126 +R R + L A+ A +R E+A+ + G PL + A F A Sbjct: 60 SRTPLNERLELLAAVCALFEKRMDEVADAITEEMGAPLAA----LSKPAQAFMGLAHFKT 115 Query: 127 GLDAKQKTPLSLPMDTFKGYILKEPIGVVGMITPWNYPLLMAVWKVAPSLAAGCTAILKP 186 L+A ++ P T + IL+EP+GV MITPWN+P+ KVAP+LA GCT +LKP Sbjct: 116 ALEAAREYPFERTRGTTR--ILREPVGVCAMITPWNWPINQIACKVAPALATGCTMVLKP 173 Query: 187 SELASLTCLELADICREVGLPPGVLNILTGLGTEAGAPLASHPHVDKIVFTGSTTTGSSI 246 SE A + A+I E G+P GV N+ G G G LASHP VD + TGST G+S+ Sbjct: 174 SEFAPYSAWIFAEILHEAGVPAGVFNMFYGDGAVVGPVLASHPLVDMVSLTGSTRAGASV 233 Query: 247 MTSAAKLVKPVSLELGGKSPIIVFDDVDIDKAVEWTMFGCFWTNGQICSATSRLLVHERI 306 +AA +K VSLELGGKS I+ + D+ KAV + GQ C+A SR+ V Sbjct: 234 SHNAADSIKRVSLELGGKSANIICESADLTKAVTHGVRSMMSNTGQSCNAPSRMYVPASR 293 Query: 307 ADEFLDKLVKWTKNIKISDPFEEGCRLGPVVSKGQYERVLKFVSNARNEGATVLCGGV-R 365 DE + + + DP + +GP+ ++ QYERV + + EGAT+LCGG R Sbjct: 294 LDEAETIAAQVCARLVVGDPRGDRTGVGPIANQRQYERVQRLIQAGIEEGATLLCGGPGR 353 Query: 366 PEHLKKGYFVEPAIVSNVTTSMEIWREEVFGPALCVKTFSTEDEAIQLANDSQYGLAGAV 425 P+ L++G++ +P + S T M I REE+FGP L ++ + +EAI+ ANDS YGL+G V Sbjct: 354 PDGLERGFYAKPTVFSRATDGMTIMREEIFGPVLTIRPYEDIEEAIRSANDSLYGLSGYV 413 Query: 426 LSNDLERCDRVSKAFQAGIVWVNCSQPCFCQAPWGGTKRSGFGRELGEWGLENYLSVKQV 485 + ++ V+K + G+V +N AP+GG K+SG GRE GE G E +L K V Sbjct: 414 YAGTVDEARAVAKRLRTGMVHLN-GASIDLAAPFGGYKQSGIGREWGEVGFEEFLETKSV 472 Lambda K H 0.318 0.135 0.421 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: 637 Number of extensions: 27 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: 503 Length of database: 479 Length adjustment: 34 Effective length of query: 469 Effective length of database: 445 Effective search space: 208705 Effective search space used: 208705 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 (21.7 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