Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__Dyella79:N515DRAFT_4224 Length = 456 Score = 270 bits (690), Expect = 8e-77 Identities = 161/431 (37%), Positives = 234/431 (54%), Gaps = 11/431 (2%) Query: 23 RLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVITVLGEIDFMLENLPEWVTA 81 R ++L AL ++ E +I AI D + EV L I L + W+ Sbjct: 16 RARRLRALNDLIGEHRGEIADAIHQDFGGRPAQETDLLEVFPSLSAIRHALAHGRRWMKP 75 Query: 82 KPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIAAGNAVIIKPSELSE 141 + +L M I+PQPLGVV II WNYP L P++ A+AAGN V++K SE + Sbjct: 76 RRSWPGLLFMPARNEIRPQPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTP 135 Query: 142 NTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNTAVGKIVMEAAAKHL 201 + + A+L +Y + V+ G + FDH+ +TG+TAVG+ VM AA+ +L Sbjct: 136 QFSALFAQLAARYFKPEEVCVVTGDADVAQAFSALPFDHLLFTGSTAVGRHVMRAASANL 195 Query: 202 TPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYILCEASLQNQIVWKI 261 TPVTLELGGKSP + RI GK N GQTCIAPDY+L + ++ V Sbjct: 196 TPVTLELGGKSPAIVGPGARFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAAA 255 Query: 262 KETVKEFYGENIKESPDYERIINLRHFKRILSL-----LEGQKIA-FGGETDE-ATRYIA 314 ++ Y + ++ + Y II+ R ++R+ +L +G K+ G ETD+ R + Sbjct: 256 RDVAARLYPQPVR-NEQYASIISERQYQRLAALRDDAARDGAKLTLLGDETDDIQRRRMT 314 Query: 315 PTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHNHKLIKRM 374 P +LT V VMQEEIFGP+LP+VP ++++AI ++ PLALY+F + L+ R+ Sbjct: 315 PALLTGVSESMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGALVDRV 374 Query: 375 IDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLLKSLKREG 434 + T++GGVT ND + H + PFGGVG SG G YHG+ F TFSH + + + + G Sbjct: 375 LARTTAGGVTINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLK-SVFRQARVNG 433 Query: 435 ANKLRYPPNSQ 445 A L PP Q Sbjct: 434 AGLLN-PPYGQ 443 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: 460 Number of extensions: 13 Number of successful extensions: 2 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: 456 Length adjustment: 33 Effective length of query: 452 Effective length of database: 423 Effective search space: 191196 Effective search space used: 191196 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 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