Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_011764036.1 AZO_RS01525 3-hydroxyacyl-CoA dehydrogenase PaaC
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_000061505.1:WP_011764036.1 Length = 515 Score = 541 bits (1394), Expect = e-158 Identities = 288/509 (56%), Positives = 358/509 (70%), Gaps = 7/509 (1%) Query: 3 ALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGK 62 ALD Q KV V+GAGAMGSGIA VAA AGH VYL+D R A + G GIAK L V+KGK Sbjct: 7 ALDKQVKVLVIGAGAMGSGIAHVAALAGHPVYLYDTRAEAIDKGIGGIAKDLAFLVEKGK 66 Query: 63 MQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNT 122 + E D V+ RI + +L D DAGL IEAI+E+L IK++L LE L DA+LA+NT Sbjct: 67 LAGAERDAVLARISGITQLADAKDAGLAIEAIVENLDIKQKLFRELEALLAEDAVLASNT 126 Query: 123 SSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKP 182 SS+S+TA+GA +++PERLVG+HFFNPAP M LVE+V GLAT + +A+ +HATA AWGK P Sbjct: 127 SSLSITAMGAALARPERLVGLHFFNPAPRMKLVEIVSGLATPRELAERMHATAKAWGKVP 186 Query: 183 VYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHD 242 V+A STPGFIVNRVARP+YAE+ R+L E A + ATLDA +RE F MG FEL DLIGHD Sbjct: 187 VHAKSTPGFIVNRVARPYYAEAQRVLAECAAEPATLDAAMREGCGFPMGPFELMDLIGHD 246 Query: 243 VNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAH 302 VN+AVT+SVF++Y+ D RF PSL+Q+ELV AGRLGRKSG GFY Y A +P P+TE H Sbjct: 247 VNFAVTNSVFDAYFGDKRFTPSLLQQELVAAGRLGRKSGHGFYSYAAGAARPAPQTEEPH 306 Query: 303 QSDESVIIAEGNPGVAAPLLERLKAAGLTIIE------RDGPGQIRFGDAVLALTDGRMA 356 ++ E+ I G GVAA L+ R +AAG+ + D G + G A +AL+DGR A Sbjct: 307 EA-EAAITVVGGLGVAAALIGRFEAAGIEVRRTAGAGGSDAQGWLEIGGARVALSDGRTA 365 Query: 357 TERAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADR 416 T RA EGV NLVLFDL DY+ RL LA ADQ A A LQ+AG+ VS I D Sbjct: 366 TRRAVEEGVPNLVLFDLCLDYATTPRLTLARADQCGHGAWGAAVGTLQRAGLAVSRIDDV 425 Query: 417 PGLVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVL 476 GLV +RTVAMLANEAADA L G+ T ADID AM+ G NYP GPL+W+D+LG V +VL Sbjct: 426 AGLVGLRTVAMLANEAADAVLQGIGTAADIDTAMRFGTNYPKGPLAWADQLGVAFVARVL 485 Query: 477 TNIQTSYAEDRYRPALLLRKNAFAQKGFY 505 N++ Y E+RYR + L+++ F+ F+ Sbjct: 486 ANLREHYGEERYRVSPLIQRKTFSGAAFH 514 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: 666 Number of extensions: 31 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: 515 Length adjustment: 35 Effective length of query: 471 Effective length of database: 480 Effective search space: 226080 Effective search space used: 226080 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