Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_011384977.1 AMB_RS13065 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::Marino:GFF2749 (506 letters) >NCBI__GCF_000009985.1:WP_011384977.1 Length = 506 Score = 312 bits (800), Expect = 2e-89 Identities = 190/491 (38%), Positives = 269/491 (54%), Gaps = 9/491 (1%) Query: 10 VAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELD 69 + +VG+G MG GIAQ+A +G V L D GAA RD ++ L + +KGK+ + Sbjct: 12 LGLVGSGTMGRGIAQIAVASGVTVILVDALPGAAAKARDAVSAMLAKLAEKGKLTAEACA 71 Query: 70 DVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTA 129 R+ L D+A +V+EAI+ED+++K+ L+ LE + + D ++A+NTSS+SVT+ Sbjct: 72 SATARLKLGESLADLAPCHVVVEAIVEDIKVKQALMKDLEAIVSKDCLIASNTSSLSVTS 131 Query: 130 LGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTP 189 + A P+R+ G HFFNP PLM +VEV+ G+ T+ V +T+ A A G PV A TP Sbjct: 132 IAAACQHPQRVGGFHFFNPVPLMKVVEVIDGVMTAPWVVETLTALARRMGHTPVKAKDTP 191 Query: 190 GFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTS 249 GF+VN R + E+L+L+ E TD T D I++ A FRMG FEL DL DV++ V Sbjct: 192 GFVVNHAGRGYGTEALKLVGEGVTDFFTADRILKGAAGFRMGPFELLDLTALDVSHPVME 251 Query: 250 SVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPY--GESAEKPQPKTEPAHQSDES 307 S+++ YYQ+PRF PS I + + AG LGRK+G+GFY Y ++ P P A Q Sbjct: 252 SIYDQYYQEPRFRPSPITRSRLVAGLLGRKTGRGFYAYEGDKAVVPPAPPVPAAWQGPVW 311 Query: 308 VIIAEGNPGVAAPLLERLKAAGLTIIERDGPGQIRFGDAVLALTDGRMATERAACEGVAN 367 V EG+ VAA L+ +L G ++ + PG+ + D A R + A Sbjct: 312 VAPGEGSLAVAA-LVTKL---GASLETGEKPGETALILIPVLGEDCTTAVVRLGLD-AAR 366 Query: 368 LVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMRTVAM 427 V D F + P +A A LL + VS+IAD PGLV R VA Sbjct: 367 SVAIDPLFGLDSHRTVMTNPVTRAE--IRDGAHGLLAGDEVAVSVIADSPGLVAQRVVAT 424 Query: 428 LANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSYAEDR 487 + N D A +AT DID A+ GL YP GPLSW DR+GA V +L + + R Sbjct: 425 IVNIGCDIAQQRIATPDDIDKAVTLGLGYPAGPLSWGDRIGAAKVVAILDTVLAITGDPR 484 Query: 488 YRPALLLRKNA 498 YR +L L++ A Sbjct: 485 YRASLWLKRRA 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: 584 Number of extensions: 30 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: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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