Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate WP_010530889.1 ON01_RS09935 aldehyde dehydrogenase
Query= BRENDA::P51648 (485 letters) >NCBI__GCF_000224785.1:WP_010530889.1 Length = 458 Score = 381 bits (979), Expect = e-110 Identities = 188/433 (43%), Positives = 286/433 (66%), Gaps = 2/433 (0%) Query: 9 RQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQEVITVLGEI 68 R FL+G++ FR +QL +L+ M++ +++I A+ DL KSE+ ++ E+ + +I Sbjct: 14 RTFFLTGKTLDPAFRKEQLTSLKGMLKSYQQEIYHALKNDLNKSEYEAFTTELGYLYTDI 73 Query: 69 DFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIAA 128 DF L++L +WV+ + V+ + ++YIQ +P GV LI+ WNYP L I P IGAIAA Sbjct: 74 DFALKHLKDWVSLEKVETPLTHKGSKSYIQKEPYGVTLIMAPWNYPLHLAIAPAIGAIAA 133 Query: 129 GNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNTA 188 GN V++KPSEL+++T+ ILA ++ D + V+ G + + +LL+QR+D+IF+TG+T Sbjct: 134 GNTVVLKPSELTQSTSTILADMIRSTFDASYFTVVEGAKDVSQQLLEQRWDYIFFTGSTN 193 Query: 189 VGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYIL 248 VGKIVME A+KHLTPVTLELGGKSP +D+D +D+ +RI WGK+ N GQTC+APDY+ Sbjct: 194 VGKIVMEQASKHLTPVTLELGGKSPAIVDQDAKIDLAAKRIVWGKFTNAGQTCVAPDYVY 253 Query: 249 CEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKIAFGGETDE 308 ++ +++ +K+ +K YG+ ++ DY RI+N +HF R+ + + +I GGE +E Sbjct: 254 VHEKVKLKLLRAMKKHIKSLYGKKPVQNYDYVRIVNKQHFDRLNAFMTDGEIIHGGEINE 313 Query: 309 ATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHNH 368 I PT+L ++ +MQEEIFGP+LP++ ++D+ I+ + E EKPLALY F N Sbjct: 314 EKLTIEPTILDKINWDDAIMQEEIFGPLLPVMTFSSLDDLISEMKEMEKPLALYYFGENE 373 Query: 369 KLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLLK 428 ++++ S GG ND + H PFGGVG+SGMGAYHGK+SFDTFSH++ L + Sbjct: 374 LKQQKLMLNVSFGGGCINDTLYHLANPHLPFGGVGNSGMGAYHGKYSFDTFSHRKSILKQ 433 Query: 429 SLKREGANKLRYP 441 + K + RYP Sbjct: 434 TTKFD--IPFRYP 444 Lambda K H 0.321 0.139 0.411 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: 569 Number of extensions: 22 Number of successful extensions: 1 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: 485 Length of database: 458 Length adjustment: 33 Effective length of query: 452 Effective length of database: 425 Effective search space: 192100 Effective search space used: 192100 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 (21.9 bits) S2: 51 (24.3 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