Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 351334 BT1806 acyl-CoA dehydrogenase (NCBI ptt file)
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Btheta:351334 Length = 568 Score = 174 bits (441), Expect = 5e-48 Identities = 121/367 (32%), Positives = 185/367 (50%), Gaps = 39/367 (10%) Query: 37 KEAIDEMAELGLFGMLVPEQWGGSDTGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPI 96 KE +D M + GL GM +P ++GG + Y M E +AA D I S+ + C+ Sbjct: 92 KENLDAMVKAGLNGMTMPRRFGGLNFPITPYTMCAEIVAAADAGFGNIWSLQD---CIET 148 Query: 97 L-RFGNEQQKEQFLTPLATGAMLGAFALTEPQAGSDASSLKTRARLEGDH--YVLNGSKQ 153 L FGN Q +F+ + G + + LTEP AGSD ++ +A ++LNG K+ Sbjct: 149 LYEFGNADQHSRFIPRVCQGETM-SMDLTEPDAGSDLQAVMLKATYSEKDGCWLLNGVKR 207 Query: 154 FITSGQNAGVVIVFAVTDPEAGK-RGISAFIVPTDSPGYQVARVEDKLGQHASDTCQIVF 212 FIT+G +A + +V A ++ RG+S FI G V R+E KLG H S TC++V+ Sbjct: 208 FITNG-DADIHLVLARSEEGTRDGRGLSMFIYDKRQGGVDVRRIEHKLGIHGSPTCELVY 266 Query: 213 DNVQVPVAN--RLGAEGEGYKIALANLEGGRIGIASQAVGMARAAFEVARDYANERQSFG 270 N + + +LG K +A + G R+GIA+Q+VG+++AA+ YA +R+ FG Sbjct: 267 KNAKAELCGDRKLGL----IKYVMALMNGARLGIAAQSVGLSQAAYNEGLAYAKDRKQFG 322 Query: 271 KPLIEHQAVAFRLADMATKISVARQMVLHAA-------ALRDAGRPALVE---------- 313 K +I+ AV LA M K+ R ++ A AL D R + Sbjct: 323 KAIIDFPAVYDMLAIMKGKLDAGRALLYQTARYVDIYKALDDISRERKLTPEERLEQKKY 382 Query: 314 -------ASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366 +AK SE A + D +Q GG G++ ++ +RIYRD R+ IYEGT+ + Sbjct: 383 AKLADSFTPLAKGMNSEYANQNAYDCIQIHGGSGFMMEYACQRIYRDARITSIYEGTTQL 442 Query: 367 QRMVIAR 373 Q + R Sbjct: 443 QTVAAIR 449 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: 435 Number of extensions: 28 Number of successful extensions: 6 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: 568 Length adjustment: 33 Effective length of query: 342 Effective length of database: 535 Effective search space: 182970 Effective search space used: 182970 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: 51 (24.3 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