Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate H281DRAFT_04595 H281DRAFT_04595 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::Marino:GFF2749 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_04595 Length = 521 Score = 299 bits (765), Expect = 2e-85 Identities = 178/492 (36%), Positives = 258/492 (52%), Gaps = 7/492 (1%) Query: 10 VAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELD 69 + +VG GAMG GIAQ+AA AG V L+D A A RD +A+ + KGK++Q Sbjct: 11 IGIVGTGAMGRGIAQIAALAGLTVRLYDANPAAIGAARDYLAETFAKLTAKGKLEQARSL 70 Query: 70 DVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTA 129 + + + D+AD LVIEAI+E L++K+ L LE + + +LA+NTSS+S+TA Sbjct: 71 AALANVTAAHAITDLADCDLVIEAIVEKLEVKQALFRELETVVSGRCVLASNTSSLSITA 130 Query: 130 LGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTP 189 + A + P R+ G HFFNP PLM +VEV+ GL + + D + A G PV A P Sbjct: 131 IAAGCTDPSRVAGYHFFNPVPLMKVVEVIDGLRSDRQAGDALMDLARRMGHTPVRAKDMP 190 Query: 190 GFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTS 249 GFIVN R E LR+ E +D I+RE FR+G FEL DL DV++ V Sbjct: 191 GFIVNHAGRGMNTEGLRVAGEGVASFVDIDRIMREQAGFRLGPFELLDLTALDVSHPVME 250 Query: 250 SVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAHQSDESVI 309 S+++ +Y++PRF PS I + G LGRK+G+GFY Y + ++ +T SV Sbjct: 251 SIYHQFYEEPRFTPSPITGTRLAGGLLGRKTGEGFYRYEDGKQQAPAETPAPAALPTSVW 310 Query: 310 IAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTD-GRMATERAACEGV--A 366 +++ ++E + AG+ + + P D+++ +T G AT A E + + Sbjct: 311 VSKRYREAYQAVVELVGKAGVKLDDGASPA----ADSLIVVTPFGHDATTAAVDEALDAS 366 Query: 367 NLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMRTVA 426 +V D F R L + AA AL G+ V++I D G V R VA Sbjct: 367 RVVAIDALFPLVGTQRRTLMTTPATTRAARDAGHALFSADGVPVTVIRDSTGFVAQRVVA 426 Query: 427 MLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSYAED 486 + N D A +AT DIDLA+ GL YP GPL+ D LGA + +L N+ + Sbjct: 427 TIVNIGCDIAQKQIATPEDIDLAVMLGLGYPRGPLALGDALGAKTILTILRNMFDVLGDP 486 Query: 487 RYRPALLLRKNA 498 RYRP+ L + A Sbjct: 487 RYRPSPWLARRA 498 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: 610 Number of extensions: 23 Number of successful extensions: 5 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: 521 Length adjustment: 35 Effective length of query: 471 Effective length of database: 486 Effective search space: 228906 Effective search space used: 228906 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