Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF1710 PGA1_c17340 acyl-CoA dehydrogenase AcdA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2985 (383 letters) >FitnessBrowser__Phaeo:GFF1710 Length = 381 Score = 259 bits (663), Expect = 7e-74 Identities = 152/378 (40%), Positives = 214/378 (56%), Gaps = 5/378 (1%) Query: 3 DIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGG 62 D L+EEQ I DMA F + IAP A+ WE G I L ++GELG + V EE GG Sbjct: 2 DFALTEEQTAIFDMAFAFGQEHIAPFARQWEAEGTIPKSLWPQIGELGFGALYVSEETGG 61 Query: 63 TYVDYVAYALAVEEISAGDGATGAFMSIHNSVGCGPVLN-YGSEEQKQTWLADLASGQVI 121 + + L E +S + AF+SIHN C +L+ + S+E K + D+ S + + Sbjct: 62 AGLSRLDATLVFEALSMACPSVAAFLSIHNM--CAKMLDSFASDEMKARIMPDILSMKTV 119 Query: 122 GCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPDLGKRG 181 +CLTEP +GS+A L+TRA + + +NG K F+S G + A V V + G +G Sbjct: 120 LSYCLTEPGSGSDAAALKTRAAKTNEGYTLNGTKAFISGGGYSD-AYVCMVRSGEDGPKG 178 Query: 182 ISAFLVPTDTAGFIVDRTEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLE 241 +S V TAG E KMG ++ T V ++C IP ANL+GE GKG A+ L+ Sbjct: 179 VSTVYVEDGTAGLSFGGLEEKMGWKSQPTAQVQFDDCKIPAANLVGEEGKGFTYAMKGLD 238 Query: 242 GGRIGIAAQALGIARAAFEAALAYSRDRVQFGKAINEHQSIANLLADMHMQLNAARLMIL 301 GGR+ IA+ +LG A+ A L Y +R FGK+I++ Q + LADM ++L AAR+ + Sbjct: 239 GGRLNIASCSLGAAQQALTMTLQYMSERKAFGKSIDQFQGLQFRLADMEIELQAARVFLR 298 Query: 302 HAARLRTAGKPCLSE-ASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVEKYYRDARIT 360 AA G P S+ + AK F +E KV +Q+HGGYGYL DY +EK RD R+ Sbjct: 299 QAAWKLDQGAPDASKHCAMAKKFVTEAGSKVVDQCLQLHGGYGYLADYGIEKLVRDLRVH 358 Query: 361 QIYEGSSEIQRMVIAREL 378 QI EG++EI R++ AR L Sbjct: 359 QILEGTNEIMRVITARHL 376 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: 348 Number of extensions: 19 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 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