Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 226 bits (577), Expect = 1e-63 Identities = 153/446 (34%), Positives = 236/446 (52%), Gaps = 24/446 (5%) Query: 45 ATEEDVDMAVKAARSALRRDDWGSTTGAQRAKYLRAIAAKVLEKKPELATLETIDNGKPW 104 ATE+ + AVKAA + W +R L+ + E++ ELA ++ GKP Sbjct: 42 ATEQAIAAAVKAAEPMRQFKPW------ERQAVLQHCVQRFTERRDELAYALCVEAGKPI 95 Query: 105 FEAASDIDDVVACFEYYADLAEALDSKKQT---EVKLHLDSFKTHVLREPLGVVGLITPW 161 ++A ++ ++ F A+ EA+ + +T E+ L+ + + R PLG V ITP+ Sbjct: 96 KDSAGEVTRLIETFGIAAE--EAVRTNGETINLEIAKRLNGYHGYTRRVPLGPVSFITPF 153 Query: 162 NYPLLMTTWKVAPALAAGCAAILKPSELASITSLELGEICREVGLPPGALSILTGLGHEA 221 N+PL + KVAPA+AAGC +LKP+E I +L +GE+ E LP GA SIL G A Sbjct: 154 NFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAFSILNLDGKHA 213 Query: 222 GSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQLVKPVTLELGGKSPIVV-FDDIHNLDTAV 280 SPLV P ++FTGS G + T A K VTLELGG + +V D + LD + Sbjct: 214 -SPLVEDPRFKLLSFTGS-QIGWDLKTRAGH--KKVTLELGGNAACIVDADQLPRLDHVI 269 Query: 281 EWTLFGCFWTNGQICSATSRLIIQETIAPQFLARLLEWTKNIKISDPLEEDCKLGPVISR 340 E +FG F+ +GQ C + R+ E++ + RL+ K +K DP +++ LGP+I Sbjct: 270 ERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKKETFLGPMIDE 329 Query: 341 GQYEKILKFISTAKDEGATILYGGDRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVL 400 E++ +I A+ G +L GG R KG ++ T++ +V ++ ++EVFGP Sbjct: 330 AAAERLHGWIEEARKGGGKVLCGGKR-----KGPMLEATLMENVRGDAKVNRQEVFGPFA 384 Query: 401 CVKTFKTEEEAIELANDTKFGLGAAILSKDLERCERFTKAFQSGIVWINCSQPCFW--QP 458 + FK+ +EAI + ND+ +GL A I + L R + G V +N P F Sbjct: 385 LLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVN-DVPSFRVDNM 443 Query: 459 PWGGKKRSGFGRELGEWSLENYLNIK 484 P+GG K SG GRE +++E+ I+ Sbjct: 444 PYGGVKLSGAGREGVRYAIEDMTEIR 469 Lambda K H 0.318 0.136 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: 538 Number of extensions: 37 Number of successful extensions: 7 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: 505 Length of database: 476 Length adjustment: 34 Effective length of query: 471 Effective length of database: 442 Effective search space: 208182 Effective search space used: 208182 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