Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_011842743.1 RSPH17029_RS19795 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000015985.1:WP_011842743.1 Length = 377 Score = 437 bits (1124), Expect = e-127 Identities = 221/374 (59%), Positives = 280/374 (74%) Query: 2 LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 ++ DEQ+ + + R FA+E L P A K + +M ELG FGM VPE+ GG Sbjct: 3 VLTDEQRLVQEMARTFAREVLAPGAAARAKAKAIEPAVLAQMGELGFFGMTVPEEMGGVG 62 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 Y++YA+AL EIAAGDGA ST+MSVHN+ + RF + Q+E+ L P A GA +GAF Sbjct: 63 ADYMSYALALIEIAAGDGAVSTVMSVHNAPFNAILQRFASPAQRERVLRPAAQGAFIGAF 122 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 ALTE AGSDAS+L++RAR G YV++G K FITSG+ AG ++FA + GK GI+ Sbjct: 123 ALTEAHAGSDASALRSRARRAGGDYVIDGEKVFITSGRLAGWAVLFARMEGSTGKEGITC 182 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 F+ PTD+PGY+V +VEDKLGQ ASDTC + FD+++VP A R+GAEGEGY+IAL++LE GR Sbjct: 183 FLTPTDTPGYEVVKVEDKLGQEASDTCALRFDSLRVPEALRIGAEGEGYRIALSSLETGR 242 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 IGIA+Q+VGMA+AA E A YA ER SFG+PLIEHQAV FRLA+ T++ ARQMVLHAA Sbjct: 243 IGIAAQSVGMAQAALEAAVAYARERTSFGRPLIEHQAVGFRLAEAKTRLEAARQMVLHAA 302 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 ++D G+P L EA+MAKLFASE AE++ SDA+QT GGYGY DFP+ERIYRDVRVCQIYE Sbjct: 303 RMKDTGQPCLTEAAMAKLFASEAAERIVSDAIQTFGGYGYSRDFPVERIYRDVRVCQIYE 362 Query: 362 GTSDIQRMVIARNL 375 GTSDIQ+M+I R + Sbjct: 363 GTSDIQKMLILRGM 376 Lambda K H 0.319 0.134 0.382 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: 440 Number of extensions: 13 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: 377 Length adjustment: 30 Effective length of query: 345 Effective length of database: 347 Effective search space: 119715 Effective search space used: 119715 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