Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 214 bits (546), Expect = 4e-60 Identities = 158/463 (34%), Positives = 235/463 (50%), Gaps = 21/463 (4%) Query: 21 VYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQV 80 V + +G V +A A+ + A+ AA A Q P R L E Sbjct: 23 VLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERRDE 82 Query: 81 FAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG----LAAGEYLEGHTSMIRR 136 A GKP+ + E+ +++ F A A NG L + L G+ RR Sbjct: 83 LAYALCVEAGKPIKDSAG-EVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRR 141 Query: 137 DPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE-LAKDIFPAG 195 PLG V+ I P+N+PL + A K+APA+AAG VLKP+E TP+ AL + E LA+ P G Sbjct: 142 VPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKG 201 Query: 196 VINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIV 255 +IL GK PL P+ +++S TGS + T + K+ +ELGG A IV Sbjct: 202 AFSILNLDGKH-ASPLVEDPRFKLLSFTGSQIGWD---LKTRAGHKKVTLELGGNAACIV 257 Query: 256 FDDAD----IEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGA 311 DAD ++ V+E + +Y +GQ C + RIYA + +YD L ++L AAV LK+G Sbjct: 258 --DADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGD 315 Query: 312 PDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQD 371 P + T LGP+ A ER+ +EEA+ G KV+ GG+++ G TL+ D Sbjct: 316 PKKKETFLGPMIDEAAAERLHGWIEEARKGGG-KVLCGGKRK---GPMLEATLMENVRGD 371 Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431 + ++EVFGP + PF + ++ + NDS YGL + ++T + A R L+ G Sbjct: 372 AKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVI 431 Query: 432 VN-THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 VN V MP+GG KLSG G++ Y +ED T +R ++++ Sbjct: 432 VNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMVMR 474 Lambda K H 0.317 0.134 0.397 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: 531 Number of extensions: 30 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: 474 Length of database: 476 Length adjustment: 33 Effective length of query: 441 Effective length of database: 443 Effective search space: 195363 Effective search space used: 195363 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: 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