Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate YP_004144004.1 Mesci_4845 acyl-CoA dehydrogenase domain-containing protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000185905.1:YP_004144004.1 Length = 387 Score = 280 bits (716), Expect = 5e-80 Identities = 150/372 (40%), Positives = 218/372 (58%) Query: 4 NDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTG 63 +++ + +RDM R FAQ+R+ P AA+ DR + FP GE LG G+ +GG G Sbjct: 11 DEEIEALRDMVRRFAQDRIAPIAADIDRSNEFPAHLWGEFGALGLLGITADPDFGGSGMG 70 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFAL 123 YLA+ +A+EEI+ + H+++ I + T QKE++L PL SG +GA A+ Sbjct: 71 YLAHVIAVEEISRASASVGLSYGAHSNLCVNQINRWATQAQKEKYLPPLCSGERVGALAM 130 Query: 124 TEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 +E AGSD LK RA D YVLNG K +IT+G +A ++V+A TDP RGI+AFI Sbjct: 131 SESGAGSDVVSLKLRAEKRNDRYVLNGTKMWITNGPDAETLVVYAKTDPDQKSRGITAFI 190 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVG 243 V G+ VA+ DKLG S+T +++F DV+VP N L EEG G + ++ L+ R Sbjct: 191 VEKAFAGFSVAQKLDKLGMRGSNTGELVFRDVEVPFDNVLHEEGRGVEVLMSGLDYERTV 250 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 +A +G+ A + A Y ER+ FG+ I E Q V +LADM T + AR V+ AA Sbjct: 251 LAGGPIGLMAACLDVAIPYVHERKQFGQAIGEFQLVQGKLADMYTTLNAARAYVYAVAAA 310 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGT 363 D G+ +A+ LFA+E A + A+Q LGG GY+ND+P R+ RD ++ +I GT Sbjct: 311 CDRGQTTRKDAAGCVLFAAEKATLMALDAIQLLGGNGYINDYPTGRLLRDAKLYEIGAGT 370 Query: 364 SDIQRMVISRNL 375 S+I+R +I R + Sbjct: 371 SEIRRWLIGREI 382 Lambda K H 0.320 0.135 0.394 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: 341 Number of extensions: 14 Number of successful extensions: 1 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: 375 Length of database: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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