Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_110806794.1 C8J30_RS15730 acyl-CoA/acyl-ACP dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >NCBI__GCF_003217355.1:WP_110806794.1 Length = 547 Score = 218 bits (554), Expect = 4e-61 Identities = 140/385 (36%), Positives = 198/385 (51%), Gaps = 14/385 (3%) Query: 6 LTEEQVMIRDMARDFARGEIAPHAQAWE-KAGWIDDALVAKMGELGLLGMVVPEEWGGTY 64 L EE MIR+ +A + P+A W K I ++ ++ +LG+ G+ +PEE+GG Sbjct: 163 LDEELEMIREQFHRYAEERVIPNAHEWHLKDELIPMEIIEELADLGVFGLTIPEEYGGLG 222 Query: 65 VDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCF 124 + + + EE+S G G+L + + +L GTEEQKQ WL LASGQ + Sbjct: 223 LSKASMVVVTEELSRGYIGVGSL-GTRSEIAAELILCGGTEEQKQKWLPGLASGQILSTA 281 Query: 125 CLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGK-KGLS 183 TEP GS+ +LRTRA WVI G K ++++ +R + + A T+PD +GLS Sbjct: 282 VFTEPNTGSDLGSLRTRAVKEGDDWVITGNKTWITHAQRTHVMTLLARTEPDTTDWRGLS 341 Query: 184 AFLV---------PTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLG-ERGKGL 233 FL P TPG E +G R + + + NLLG E G+G Sbjct: 342 MFLAEKTPGTDENPFPTPGMTGGEIE-VLGYRGMKEYELGFDGFRVKGENLLGGETGRGF 400 Query: 234 AIALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRL 293 + E RI AA+A+G+A+AA E + YA DR QF K +IE V LA M + Sbjct: 401 KQLMETFESARIQTAARAVGVAQAACEIGMRYAIDRKQFGKSLIEFPRVGGKLAMMAVEI 460 Query: 294 NAARLLILHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERY 353 AR L +A + G C EA AKL + +A +A+QIHGG G+ +Y + R Sbjct: 461 MIARQLTYFSAWEKDHGHRCDVEAGMAKLLGARVAWAASDNALQIHGGNGFALEYTISRI 520 Query: 354 YRDARITQIYEGSSEIQRMVIAREL 378 DARI I+EG++EIQ VIAR L Sbjct: 521 LCDARILNIFEGAAEIQAQVIARRL 545 Lambda K H 0.319 0.134 0.394 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: 425 Number of extensions: 22 Number of successful extensions: 4 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: 547 Length adjustment: 33 Effective length of query: 350 Effective length of database: 514 Effective search space: 179900 Effective search space used: 179900 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