Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate PP_3282 PP_3282 3-hydroxyadipyl-CoA dehydrogenase
Query= reanno::Marino:GFF2749 (506 letters) >FitnessBrowser__Putida:PP_3282 Length = 505 Score = 597 bits (1540), Expect = e-175 Identities = 305/496 (61%), Positives = 386/496 (77%), Gaps = 1/496 (0%) Query: 1 MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDK 60 M AL + +VAV+GAGAMG+GIAQVAAQAGH V L+D R GAA GI +QL R VDK Sbjct: 1 MAALASNVQVAVIGAGAMGAGIAQVAAQAGHPVKLYDNRPGAAAQAVTGIDRQLARLVDK 60 Query: 61 GKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILAT 120 GK+ E + + R+ PV L+ +ADAGLVIEAI+E+LQ+K+ L + LE LC AD ILA+ Sbjct: 61 GKLLAAERETINARLCPVDTLEALADAGLVIEAIVENLQVKQALFSQLETLCAADCILAS 120 Query: 121 NTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGK 180 NTSS+S+T+L A + +P+ +VGMHFFNPAPLMALVEVV GLAT VA ++ATA AWGK Sbjct: 121 NTSSLSITSLAAGLERPQHVVGMHFFNPAPLMALVEVVSGLATDPAVAACIYATAQAWGK 180 Query: 181 KPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIG 240 +PV+A STPGFIVNRVARPFYAESLRLLQE A D A+LDA++R++G FRMGAFELTDLIG Sbjct: 181 QPVHARSTPGFIVNRVARPFYAESLRLLQEGAADCASLDALMRDSGGFRMGAFELTDLIG 240 Query: 241 HDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEP 300 HDVNYAVT SVF+++Y D RF PSL+QKELV+AG LGRK+GQGFY Y E E+PQP Sbjct: 241 HDVNYAVTCSVFDAFYGDFRFQPSLVQKELVDAGHLGRKTGQGFYRYAEGVERPQPAELH 300 Query: 301 AHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERA 360 + E+ ++ EGN GV PL+ERL+ +G+ + +R G G I+ GDA LAL+DGR+A++RA Sbjct: 301 SSACAEACVV-EGNLGVMQPLVERLRQSGIAVTQRAGSGLIQVGDATLALSDGRLASQRA 359 Query: 361 ACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLV 420 +G+ NLVL DLA DYS A+R+A++ + SD+A A ALLQ+AG++V+ +AD PGLV Sbjct: 360 REDGLRNLVLLDLALDYSSATRIAISWSADTSDSARDQAVALLQRAGLKVTGVADLPGLV 419 Query: 421 IMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQ 480 ++RTVAMLANEAADA L GV + ADIDLAM+AG+NYP GPL+W+ +G H +VL N+Q Sbjct: 420 VLRTVAMLANEAADAVLQGVGSAADIDLAMRAGVNYPCGPLAWAANIGIAHTLRVLDNLQ 479 Query: 481 TSYAEDRYRPALLLRK 496 SY E RYRP+LLLR+ Sbjct: 480 CSYGESRYRPSLLLRR 495 Lambda K H 0.318 0.133 0.375 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: 702 Number of extensions: 23 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: 506 Length of database: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 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