Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_073037063.1 BUB04_RS03730 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_900129305.1:WP_073037063.1 Length = 382 Score = 355 bits (912), Expect = e-103 Identities = 191/379 (50%), Positives = 259/379 (68%), Gaps = 2/379 (0%) Query: 1 MHDLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEW 60 MH EL+E+QRMI+DMAR FA REIAP A ++ + +V +MGELGL+G+ +P E+ Sbjct: 1 MH-FELTEEQRMIQDMARKFAEREIAPVAAELDRTHKHPEEIVKKMGELGLMGITIPPEY 59 Query: 61 GGSYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRA 120 GG+ +DYV+Y LA+ EIS + G +MS+ NS+ PV YG++ QK ++LT +ASG Sbjct: 60 GGAGMDYVSYVLAMIEISKACASCGVIMSVCNSLYNFPVYTYGTEEQKQQFLTPVASGEY 119 Query: 121 IGCFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKK 180 +GC+ LTE AGS+ +RT A L WV+NG K+F +N ++ ++ AVTD E G K Sbjct: 120 LGCYGLTEAGAGSDPAKMRTTAVLDGNEWVINGEKKFITNGNVARYCVLAAVTDKEKGYK 179 Query: 181 GLSAFLVPT-DTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSN 239 G+S+FLV +TPGF V R E K+GI AS T + D RIP+ NLLG+ G+G L+ Sbjct: 180 GISSFLVDLHNTPGFKVGRVEEKLGINASGTAELIFEDARIPKENLLGKEGEGFKQMLTT 239 Query: 240 LEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLL 299 L+GGRIGI +QA+GI RA E A+ YA+ R QFG+PIA Q+I LAD+ TQL+AA LL Sbjct: 240 LDGGRIGIASQAIGIGRAVLEEAIEYAKTREQFGRPIASFQAIQWKLADIATQLDAAELL 299 Query: 300 ILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARI 359 L AA L+ G EA+ AKLFAS+ A + VQI GGYGY ++YP+ER+ RDA+I Sbjct: 300 TLRAAWLEQNGRGYEKEAAMAKLFASDTAMWAAVEGVQILGGYGYCKEYPMERHMRDAKI 359 Query: 360 TQIYEGSSEIQRLLIAREL 378 TQIYEG++EI RL+I+R + Sbjct: 360 TQIYEGTNEIMRLVISRNI 378 Lambda K H 0.318 0.133 0.390 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: 364 Number of extensions: 10 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 ( 7.3 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 Apr 09 2024. 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