Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Echvi_1073 Echvi_1073 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Cola:Echvi_1073 Length = 599 Score = 220 bits (561), Expect = 7e-62 Identities = 136/390 (34%), Positives = 212/390 (54%), Gaps = 27/390 (6%) Query: 5 DEQQQIADAVRAFAQERLKPFAEQWD--KDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 +EQ+ +A A + F + P +E+ D K+ + + ELGL G+ VPE++ G Sbjct: 31 EEQRMMAQACQDFIDTEILPKSEEIDSMKNPDLVPAILKKAGELGLLGISVPEEYQGLGM 90 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 + +M + +I G+ ST H +G +PIL +G E+QK+++L LATG + Sbjct: 91 SFNT-SMLIADIIGAAGSFSTTYGAHTGIGTLPILYYGTEEQKKKYLPKLATGEWAACYC 149 Query: 123 LTEPQAGSDASSLKTRARL--EGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGIS 180 LTEP AGSDA+S KT+A L +G HY+LNG K +I++G A + IVFA + + ++ Sbjct: 150 LTEPDAGSDANSGKTKATLTEDGKHYLLNGQKMWISNGGFADLFIVFAKIGED---KNLT 206 Query: 181 AFIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGG 240 AFIV D G + E K+G S T Q+ F++ +VPV N L G+KIA+ L G Sbjct: 207 AFIVEKDFGGITMNEEEKKMGIKGSSTRQVFFNDCKVPVENMLSDRQNGFKIAVNILNIG 266 Query: 241 RIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHA 300 R+ + + +G R + A Y++ER+ FG + A+ +LA+MA K V+ + Sbjct: 267 RVKLGAGVLGGCRQVIKNALQYSSERKQFGVSINTFGAIKSKLAEMAVKTYVSESLCYRL 326 Query: 301 A--------ALRDAGRPA-----------LVEASMAKLFASEMAEKVCSDALQTLGGYGY 341 AL +G A +E ++AK+ SE+ + V +Q GG GY Sbjct: 327 GQNIEDRIDALMASGMEANQAKLKGVEQFAMECAIAKIHGSEVLDYVVDQGVQIYGGMGY 386 Query: 342 LSDFPLERIYRDVRVCQIYEGTSDIQRMVI 371 +D P+ER YRD R+ +IYEGT++I RM++ Sbjct: 387 SADAPMERAYRDARISRIYEGTNEINRMLM 416 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: 521 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 599 Length adjustment: 33 Effective length of query: 342 Effective length of database: 566 Effective search space: 193572 Effective search space used: 193572 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