Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate HSERO_RS20645 HSERO_RS20645 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::Marino:GFF2749 (506 letters) >FitnessBrowser__HerbieS:HSERO_RS20645 Length = 512 Score = 458 bits (1178), Expect = e-133 Identities = 250/498 (50%), Positives = 325/498 (65%), Gaps = 8/498 (1%) Query: 3 ALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGK 62 AL VAV+G+G MG+GIAQVAA AGH V L+D REGAA I L + V K K Sbjct: 9 ALSRSALVAVIGSGTMGAGIAQVAAVAGHPVLLYDSREGAAGKAIGAICTNLDKLVSKDK 68 Query: 63 MQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNT 122 + RI L+++ A LVIEAI+E L K +L LE + + ILATNT Sbjct: 69 LTPALAQAASQRISVAQSLEELHQADLVIEAIVEQLAAKHELFGKLEAIVSTRCILATNT 128 Query: 123 SSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKP 182 SS+S+T + A + PER+VGMHFFNP P+MALVE++ GLA+ +A +H TA AWGK P Sbjct: 129 SSLSITQIAAGLQHPERVVGMHFFNPVPMMALVEIISGLASDAALAQCLHDTALAWGKTP 188 Query: 183 VYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHD 242 V A STPGFIVNR+ARP+YAE LR+L E AT+DA++REAG FRMG FEL DLIGHD Sbjct: 189 VMARSTPGFIVNRLARPYYAEGLRMLHEGGAQPATIDAVMREAGGFRMGPFELMDLIGHD 248 Query: 243 VNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAH 302 VN+AVT SVF++Y+ DPRF PSLIQ+ELV AG LGRKSG+GFY YGE+A P+P+TE + Sbjct: 249 VNFAVTQSVFHAYFNDPRFTPSLIQQELVHAGYLGRKSGRGFYRYGEAAGAPRPETERDY 308 Query: 303 QSDESVIIAEGNPGVAAPLLERLKAAGLTIIERD--GPGQI--RFGDAVLALTDGRMATE 358 + G+ PL+E + ++R P Q+ + A L +TDGR AT Sbjct: 309 PKPTATPQLYGD----HPLVEMIHTRYPGQVQRHPARPDQLLMKVNAACLCITDGRSATL 364 Query: 359 RAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPG 418 RA +LVL DLA DY+ A+RLALA ADQ + +LQ G+++S + D PG Sbjct: 365 RAWEHQEPDLVLVDLALDYADATRLALAKADQCRPQRYAEVAGVLQACGLDLSPMQDVPG 424 Query: 419 LVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTN 478 +++MRTV ML NEAADA GV AD D+AM+ G+NYP GPL+W++ +G V +VL + Sbjct: 425 MMVMRTVCMLVNEAADAVNQGVCNAADADMAMRKGVNYPRGPLAWANEIGIDTVNQVLHH 484 Query: 479 IQTSYAEDRYRPALLLRK 496 + +Y EDRYR + LL++ Sbjct: 485 LCATYGEDRYRISPLLQR 502 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: 661 Number of extensions: 26 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: 512 Length adjustment: 34 Effective length of query: 472 Effective length of database: 478 Effective search space: 225616 Effective search space used: 225616 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