Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_011766765.1 AZO_RS15265 3-hydroxyacyl-CoA dehydrogenase PaaC
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_000061505.1:WP_011766765.1 Length = 508 Score = 554 bits (1427), Expect = e-162 Identities = 288/507 (56%), Positives = 370/507 (72%), Gaps = 5/507 (0%) Query: 1 MPALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDK 60 M AL KVAVVGAGAMGSGIA VAA+AGH VYL+D A G+ GI K L+ V K Sbjct: 1 MAALAHSIKVAVVGAGAMGSGIAHVAARAGHTVYLYDMNAEAVARGKAGIEKDLRFLVGK 60 Query: 61 GKMQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILAT 120 GK+ + + + + R+ P ++++D+ADAGL+IEAI+E+L+IK++L LE++ + AILAT Sbjct: 61 GKLSEADCEATLARVQPTSRIEDLADAGLLIEAIVENLEIKQKLFRQLEEMVGSGAILAT 120 Query: 121 NTSSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGK 180 NTSS+S+TA+G+ +++P++L G+HFFNPAP MALVE+V GLAT VA T++ TA AWGK Sbjct: 121 NTSSLSITAMGSALARPQQLAGLHFFNPAPRMALVEIVSGLATDPAVAATLYDTAKAWGK 180 Query: 181 KPVYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIG 240 PV+ATSTPGFIVNRVARP+YAE+LR+L E+A ATLDAI+REA F MG FEL DLIG Sbjct: 181 VPVHATSTPGFIVNRVARPYYAEALRVLAERAATPATLDAIMREACNFPMGPFELMDLIG 240 Query: 241 HDVNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEP 300 HDVNYAVT SVF++Y+ D RF PSLIQ+EL AGRLGRKSGQGFY Y + A+KPQP EP Sbjct: 241 HDVNYAVTRSVFDAYFGDKRFTPSLIQQELTLAGRLGRKSGQGFYDYRDGADKPQPAVEP 300 Query: 301 AHQSDESVIIAEGNPGVAAPLLERLKAAGLTIIERDGP----GQIRFGDAVLALTDGRMA 356 H + + G+ GVAAPLL RL+AAG+ I G G++ GDA L ++DGR A Sbjct: 301 -HAAPAKAVSVSGDLGVAAPLLARLEAAGIPIEHCAGAPSHGGELLIGDARLLMSDGRTA 359 Query: 357 TERAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADR 416 T RAA EG +LVLFDLA DY+ R+ALA ADQ + A LQ AGI VS + D Sbjct: 360 THRAAEEGTPDLVLFDLARDYATTPRIALARADQCGEEAWQLVVGTLQAAGIAVSRLDDV 419 Query: 417 PGLVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVL 476 GLV +RTV MLANEAAD + G+ + ADID AM+ G NYP+GPL+W+DRLG V +VL Sbjct: 420 AGLVALRTVCMLANEAADGVVQGIGSAADIDTAMRYGTNYPEGPLAWADRLGVDFVARVL 479 Query: 477 TNIQTSYAEDRYRPALLLRKNAFAQKG 503 TN++ Y E+RYR + L+++ A+ ++G Sbjct: 480 TNLRAHYGEERYRLSPLIQRRAYGRRG 506 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: 662 Number of extensions: 30 Number of successful extensions: 4 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: 508 Length adjustment: 34 Effective length of query: 472 Effective length of database: 474 Effective search space: 223728 Effective search space used: 223728 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