Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_057507944.1 ABB28_RS06925 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2985 (383 letters) >NCBI__GCF_001431535.1:WP_057507944.1 Length = 382 Score = 346 bits (887), Expect = e-100 Identities = 182/375 (48%), Positives = 257/375 (68%), Gaps = 1/375 (0%) Query: 3 DIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGG 62 D +EEQ+M++D+AR A+ +IAP A+ ++ G + +GE GL+G+ VP E+GG Sbjct: 2 DFSFTEEQLMLQDVARRIAQEKIAPSAEHHDRTGEFPLANIQLLGENGLMGIEVPAEYGG 61 Query: 63 TYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLNYGSEEQKQTWLADLASGQVIG 122 +D +AY LA+ E++AGD A MS++NS+ C +L +G+E QKQ ++ +A G IG Sbjct: 62 AGMDPIAYVLAMVEVAAGDAAHSTIMSVNNSLFCNGILTHGNEAQKQKYVRAIAEGTAIG 121 Query: 123 CFCLTEPQAGSEAHNLRTRA-ELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPDLGKRG 181 F LTEPQ+GS+A +R RA + DG +VING K ++++G AK ++FA+TD D G RG Sbjct: 122 AFALTEPQSGSDATAMRCRAVKQADGSYVINGKKSWITSGPVAKYIVLFAMTDADKGARG 181 Query: 182 ISAFLVPTDTAGFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLE 241 ISAFL+ TD AGF +TE K+GIRAS TC + N+ +LLG+ G+G IA+ L+ Sbjct: 182 ISAFLIDTDNAGFGRGKTEPKLGIRASATCEIEFNDYVAQAEDLLGQEGEGFKIAMGVLD 241 Query: 242 GGRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHMQLNAARLMIL 301 GRIGIA+QA+GIARAA+EA L Y ++R FG AI Q +ADM +L+AA L+ L Sbjct: 242 AGRIGIASQAIGIARAAYEATLEYVKERKAFGAAIGTFQMTQAKIADMKCKLDAALLLTL 301 Query: 302 HAARLRTAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVEKYYRDARITQ 361 AA ++ GK +EA+ AKL ASE A + A+QIHGG GY ++ P+E+Y+RDA+IT+ Sbjct: 302 RAAWVKGEGKRFSNEAAIAKLTASEAAMWITHQAVQIHGGMGYSKEMPLERYFRDAKITE 361 Query: 362 IYEGSSEIQRMVIAR 376 IYEG+SEIQR+VIAR Sbjct: 362 IYEGTSEIQRLVIAR 376 Lambda K H 0.319 0.134 0.393 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: 359 Number of extensions: 16 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: 383 Length of database: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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