Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF1190 PGA1_c12060 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2985 (383 letters) >FitnessBrowser__Phaeo:GFF1190 Length = 383 Score = 220 bits (561), Expect = 5e-62 Identities = 128/379 (33%), Positives = 201/379 (53%), Gaps = 3/379 (0%) Query: 2 HDIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWG 61 H +++E M+ DM F E AP + W K G +D + G LGLL VPEE+G Sbjct: 6 HSSWMTDEHQMLADMTAQFITREWAPKFETWRKQGMMDRSTWNEAGALGLLCPSVPEEYG 65 Query: 62 GTYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLNYGSEEQKQTWLADLASGQVI 121 G D+ A + E S + A+ IH+ + VL+YG+EEQKQ WL + +G+++ Sbjct: 66 GVGGDFGHEAAILIEGSRANLASWGH-GIHSGIVAHYVLSYGTEEQKQRWLPKMITGELV 124 Query: 122 GCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPDLGKRG 181 G +TEP GS+ ++T+A + ++G K F++NG+ A L +V A TDP G +G Sbjct: 125 GALAMTEPSTGSDVQRIKTKAVKDGNAYRLSGQKTFITNGQHANLILVAAKTDPSQGSKG 184 Query: 182 ISAFLVPTDTA-GFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLL-GERGKGLAIALSN 239 IS V TD A GF R K+G+ A+DT + +N I N+L G G+G + Sbjct: 185 ISLVAVETDGADGFSRGRNLDKIGLHAADTSELFFDNVEIAPENILGGTEGQGFYQMMQQ 244 Query: 240 LEGGRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHMQLNAARLM 299 L R+ IA A+G A E + Y ++R FG + + Q+ L + + AR Sbjct: 245 LPQERLIIACGAVGAMEGAVERTITYCKEREAFGGPLTQFQNTRFKLVECQTKTKVARAF 304 Query: 300 ILHAARLRTAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVEKYYRDARI 359 + GK + +A+ AK + ++ V +Q+HGGYG++++Y V + + DAR+ Sbjct: 305 LDECMVEHLQGKLTVEKAAMAKYWITDTQGDVLDECVQLHGGYGFMQEYAVAEMWTDARV 364 Query: 360 TQIYEGSSEIQRMVIAREL 378 +IY G++EI + +IAR L Sbjct: 365 QRIYGGTNEIMKELIARSL 383 Lambda K H 0.319 0.134 0.393 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: 355 Number of extensions: 15 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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 17 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