Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_057507944.1 ABB28_RS06925 acyl-CoA dehydrogenase
Query= reanno::Phaeo:GFF1011 (386 letters) >NCBI__GCF_001431535.1:WP_057507944.1 Length = 382 Score = 282 bits (722), Expect = 1e-80 Identities = 158/376 (42%), Positives = 222/376 (59%), Gaps = 1/376 (0%) Query: 6 MTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFG 65 M F E+ L+D+ R AQE++ P A+ D+ EFP Q +GE GL+GI VP E+G Sbjct: 1 MDFSFTEEQLMLQDVARRIAQEKIAPSAEHHDRTGEFPLANIQLLGENGLMGIEVPAEYG 60 Query: 66 GAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHV 125 GAGM +A+ +A+ E+A A+ S +++L N I +GN QK KY+ + G + Sbjct: 61 GAGMDPIAYVLAMVEVAAGDAAHSTIMSVNNSLFCNGILTHGNEAQKQKYVRAIAEGTAI 120 Query: 126 GALAMSEAGAGSDVVSMSLRAEKRND-HYRLNGNKYWITNGPDADTLVVYAKTDPDAGSK 184 GA A++E +GSD +M RA K+ D Y +NG K WIT+GP A +V++A TD D G++ Sbjct: 121 GAFALTEPQSGSDATAMRCRAVKQADGSYVINGKKSWITSGPVAKYIVLFAMTDADKGAR 180 Query: 185 GMTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGL 244 G++AFLI+ + GF + KLG+R S T E+ F D E++LG+EG+G ++ M L Sbjct: 181 GISAFLIDTDNAGFGRGKTEPKLGIRASATCEIEFNDYVAQAEDLLGQEGEGFKIAMGVL 240 Query: 245 DYERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYV 304 D R+ +A GI A + + Y+KERK FG IG FQ+ Q KIADM ++ A Sbjct: 241 DAGRIGIASQAIGIARAAYEATLEYVKERKAFGAAIGTFQMTQAKIADMKCKLDAALLLT 300 Query: 305 YEVAKACDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLM 364 A +G +AA L ASE AM HQAVQ GG GY + P+ R FRDAK+ Sbjct: 301 LRAAWVKGEGKRFSNEAAIAKLTASEAAMWITHQAVQIHGGMGYSKEMPLERYFRDAKIT 360 Query: 365 EIGAGTSEIRRMLIGR 380 EI GTSEI+R++I R Sbjct: 361 EIYEGTSEIQRLVIAR 376 Lambda K H 0.318 0.132 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: 387 Number of extensions: 22 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: 386 Length of database: 382 Length adjustment: 30 Effective length of query: 356 Effective length of database: 352 Effective search space: 125312 Effective search space used: 125312 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: 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