Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_086509764.1 BZY95_RS09860 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_002151265.1:WP_086509764.1 Length = 383 Score = 295 bits (756), Expect = 1e-84 Identities = 163/369 (44%), Positives = 228/369 (61%), Gaps = 2/369 (0%) Query: 9 QISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYA 68 Q+ D +F +ERL P A E P E + EM E+G FG+ +PE++GG A Sbjct: 10 QLIDTISRFVRERLIPNEARLAEEDAVPAELLEEMKEMGLFGLSIPEEYGGLGLTMEEEA 69 Query: 69 MALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQA 128 + EI A +I +N +G IL G +QK +++ LA+G +L +F LTEP A Sbjct: 70 LVAMEIGKTSPAFRSIFGTNNGIGAQGILIDGTPEQKAKYVPRLATGELLSSFCLTEPDA 129 Query: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDP-SAGKRGISAFIVPTD 187 GSDA+SL+T A +GDHYVLNG K+FIT+G A V V A TDP + G GI+AFIV D Sbjct: 130 GSDAASLRTTAVRDGDHYVLNGTKRFITNGPEADVFTVMARTDPGNKGAGGITAFIVEGD 189 Query: 188 SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYKIALANLEGGRVGIAS 246 +PG K + K+GQ + TC I+FED +VP N +G EG+G+K A+ L+ GR+ I++ Sbjct: 190 TPGLKRGPADSKMGQKGAHTCDIIFEDCRVPAENIIGGVEGKGFKTAMKVLDRGRLHISA 249 Query: 247 QSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDS 306 VG+A E + +YA ER+ FG P+ EHQ V LAD T+ R MV AA +D+ Sbjct: 250 VCVGVAERLVEESLNYAIERKQFGVPLAEHQLVQAMLADSKTEAYAGRTMVLDAARRKDA 309 Query: 307 GKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDI 366 G+ A AS KLF +EM +V A+Q GG GY++++ +ER YRDVR+ +IYEGT+ I Sbjct: 310 GENASTLASCCKLFCAEMVGRVADRAVQVHGGAGYMAEYAVERFYRDVRLFRIYEGTTQI 369 Query: 367 QRMVISRNL 375 Q++VI+RN+ Sbjct: 370 QQVVIARNM 378 Lambda K H 0.319 0.134 0.389 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: 343 Number of extensions: 19 Number of successful extensions: 3 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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