Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_012334305.1 M446_RS21930 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000019365.1:WP_012334305.1 Length = 560 Score = 229 bits (585), Expect = 1e-64 Identities = 143/390 (36%), Positives = 208/390 (53%), Gaps = 15/390 (3%) Query: 2 DFNFNEDQRQFADLARQFAADELAPFAAKWDEEH-HFPKDVIQKAGELGFCSLYSPESEG 60 D +ED R+F E+ P A +W +++ + P ++I + ELG L PE G Sbjct: 171 DSGLDEDMEAIRTEMRRFGQAEVVPHAHEWHQQNAYIPLEIIGQMAELGVFGLTIPEEYG 230 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 GMGL ++ ++ EELS+ ++ T +A ++ GT+ +Q + + +G++L Sbjct: 231 GMGLPKISMCVVSEELSRAYIGVGSLGTRSEIAAELILCGGTEAQKQRFLPKIASGEILP 290 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRT--GQAGPKG 178 + TEP GSD A+L+TKAVREGD + V G+K +I+ +L+ ++ RT + G +G Sbjct: 291 TAVFTEPNTGSDLANLRTKAVREGDTWKVYGNKTWITHPVRADLMTILVRTKPEEPGHRG 350 Query: 179 ISAI---------AIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGE-EGQ 228 +S + A P G+ G+ E +G+ + FD VP ANLLGE EG+ Sbjct: 351 LSLLLGEKPRGSDAEPFPVAGLSGGEIE-VLGYRGMKEYELAFDGFEVPAANLLGEVEGK 409 Query: 229 GFTFAMKGLDGGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMAT 288 GF M+ + RI A +VG AQ+AL+ +Y ER QFGKPL AF + KLA MA Sbjct: 410 GFAQLMQTFESARIQTAARAVGVAQSALDIGLRYAEERVQFGKPLVAFPRVADKLAMMAV 469 Query: 289 ELVAARQMVRLAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPL 348 E+ ARQ+ AA + D G MAK A V + D ALQIHGG G+ EY + Sbjct: 470 EIAIARQLTYFAAHEKDEG-KRCDLEAGMAKLLAARVAWAAADNALQIHGGNGFALEYQI 528 Query: 349 ERHFRDVRVHQILEGTNEIMRLIIARRLLD 378 R D R+ I EG EI +IARRLL+ Sbjct: 529 SRVLCDARILSIFEGAAEIQAQVIARRLLE 558 Lambda K H 0.320 0.134 0.396 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: 501 Number of extensions: 25 Number of successful extensions: 5 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: 385 Length of database: 560 Length adjustment: 33 Effective length of query: 352 Effective length of database: 527 Effective search space: 185504 Effective search space used: 185504 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 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