Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_084019521.1 K420_RS0101380 3-hydroxyacyl-CoA dehydrogenase PaaC
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_000519045.1:WP_084019521.1 Length = 519 Score = 531 bits (1367), Expect = e-155 Identities = 291/504 (57%), Positives = 356/504 (70%), Gaps = 3/504 (0%) Query: 4 LDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKM 63 L Q VAVVG GAMG+GIAQVAAQAGH V L D R GAA DGI Q + +KGK+ Sbjct: 16 LSQQAVVAVVGTGAMGAGIAQVAAQAGHVVKLLDNRSGAAAKAVDGIRAQFAKLAEKGKI 75 Query: 64 QQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTS 123 + R+ V +L D+ADA LV+EAI+E+L+ K++L A LE + +AD I TNTS Sbjct: 76 SAEAAQAAGDRLVAVEQLADLADAALVVEAIVENLEAKQKLYADLEGIVSADCIFGTNTS 135 Query: 124 SISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPV 183 SISVTA+GA + +PERL G+HFFNPAPLMALVE+V GLAT K VA+T+ ATA AWGK V Sbjct: 136 SISVTAIGAALQRPERLAGLHFFNPAPLMALVEIVSGLATDKVVAETLFATANAWGKTAV 195 Query: 184 YATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDV 243 +A STPGFIVNRVARP+YAE+LR+ QE A D AT+DA REAG FRMG FEL D+IGHDV Sbjct: 196 HAKSTPGFIVNRVARPYYAEALRIAQEGAADYATIDACCREAGGFRMGPFELMDMIGHDV 255 Query: 244 NYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQ 303 N+AVT+SV+ ++Y D RFLPSLIQ+ELV+AG GRKSG+GFY Y E A KP P+TE A Q Sbjct: 256 NFAVTNSVWRAFYNDQRFLPSLIQQELVDAGFYGRKSGRGFYDYREGAVKPVPQTE-APQ 314 Query: 304 SDESVIIAEGNPGVAAPLLERLKAAGLTIIER-DGPGQI-RFGDAVLALTDGRMATERAA 361 + I G VA L+ERL+ +GL+ D G+I G A L +TDGR AT+RAA Sbjct: 315 TPAGKITVFGECAVAEALVERLQHSGLSFGRAPDADGRIAEIGLAKLYVTDGRSATQRAA 374 Query: 362 CEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVI 421 GVAN VL DLA DYSKA+RLA+A A+Q AAV A LLQ AG VS D PGL++ Sbjct: 375 ETGVANTVLIDLALDYSKATRLAVAAAEQCEPAAVVSAVGLLQAAGFAVSRFLDVPGLLV 434 Query: 422 MRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQT 481 MRTVAMLANEAADA GV T D AM+ G+NYP GPL+W+D++G + VL N+ Sbjct: 435 MRTVAMLANEAADAVNQGVCTEKGADQAMRLGVNYPQGPLAWADQVGVAAIRDVLANLGA 494 Query: 482 SYAEDRYRPALLLRKNAFAQKGFY 505 SY EDRYR + L+++ FA + + Sbjct: 495 SYGEDRYRISPLIQRAVFAGRNIH 518 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: 679 Number of extensions: 21 Number of successful extensions: 3 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: 519 Length adjustment: 35 Effective length of query: 471 Effective length of database: 484 Effective search space: 227964 Effective search space used: 227964 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 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