Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_057507563.1 ABB28_RS04915 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_001431535.1:WP_057507563.1 Length = 388 Score = 514 bits (1324), Expect = e-150 Identities = 257/378 (67%), Positives = 297/378 (78%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 M E Q+ + + AR FA ELAP AA+WD E FP++ I KAGELGFC LY G Sbjct: 5 MTTELEEAQQAYREAARDFAQAELAPHAARWDAEGIFPREAIAKAGELGFCGLYMDPEVG 64 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 G GLSRLDA+++ EEL+ +T A ++IHNMA+WMV+TWG LR AW L G LA Sbjct: 65 GSGLSRLDAAVVIEELANVDPSTAAYVSIHNMASWMVSTWGQQALRAAWGADLAAGIRLA 124 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGIS 180 SYCLTEPGAGSDAASL+T AVR+GD+YV++GSK FISGAG+TELLVVM RTG AG GIS Sbjct: 125 SYCLTEPGAGSDAASLKTTAVRDGDDYVLNGSKAFISGAGATELLVVMARTGGAGAGGIS 184 Query: 181 AIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGG 240 AIA+PAD GI YG+ E+KMGWN+QPTR +TF+NVRVPV NLLGEEG GF AMKGLDGG Sbjct: 185 AIAVPADLPGISYGRKEEKMGWNSQPTRGITFENVRVPVGNLLGEEGGGFKLAMKGLDGG 244 Query: 241 RINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLA 300 RINIA CS+G AQ AL+ A +YM ER+QFGK LA FQALQFKLADMA ELVAARQMV A Sbjct: 245 RINIAACSLGAAQGALDAARRYMGERRQFGKALAEFQALQFKLADMAIELVAARQMVHTA 304 Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360 A KLD+G +A +CAMAKRFATD GF +C+ ALQIHGGYGYIREYP+ER RD RVHQI Sbjct: 305 ARKLDAGASDANVWCAMAKRFATDAGFTICNEALQIHGGYGYIREYPIERLLRDSRVHQI 364 Query: 361 LEGTNEIMRLIIARRLLD 378 LEGTNEIMR+I+AR LL+ Sbjct: 365 LEGTNEIMRVIVARHLLN 382 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: 482 Number of extensions: 14 Number of successful extensions: 1 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: 388 Length adjustment: 30 Effective length of query: 355 Effective length of database: 358 Effective search space: 127090 Effective search space used: 127090 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