Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_015945287.1 DHAF_RS22620 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_000021925.1:WP_015945287.1 Length = 591 Score = 241 bits (616), Expect = 3e-68 Identities = 151/401 (37%), Positives = 223/401 (55%), Gaps = 29/401 (7%) Query: 5 ELSEDQRMIRDMARDFARREIAPHAQAWEKA--GWIDDTLVAQMGELGLLGMVVPEEWGG 62 EL+ED ++ M R+F +EI P +A E+ G I D +AQ GELGLLG+ VPEE GG Sbjct: 27 ELNEDHLQLKKMTRNFVEKEIGPKIEALEEQEDGLIRD-FMAQAGELGLLGLEVPEELGG 85 Query: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 +D + + EEI G A M+ H +G P++ +G+ QK ++L LA+G I Sbjct: 86 MSMDKFSTVVVGEEIPRGASFAVAFMA-HTGIGTLPIVYFGTPEQKAKYLPGLATGEKIA 144 Query: 123 CFALTEPQAGSEAHNLRTRAEL-VDG-HWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKK 180 + LTEP +GS+A + A L +G H++LNG+KQF +NA + + +V+A + GK Sbjct: 145 AYCLTEPGSGSDALGAKATAVLNAEGTHYLLNGTKQFITNAGFADIFLVYAKVE---GK- 200 Query: 181 GLSAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNL 240 L+ F+V PG + E KMGI+ S T V L D +P N++GE G+G +A + L Sbjct: 201 -LTNFIVERTMPGLSFGPEEKKMGIKGSSTRQVILEDVAVPVENIVGELGRGHVVAFNIL 259 Query: 241 EGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLI 300 GR + A A+G A+ A E L YA ER QFG P++ +I A++ Q A ++ Sbjct: 260 NVGRFKLAAAAIGSAQLALEVTLKYAAERKQFGVPLSSFGAIQTKFAEIAAQTYLAESVV 319 Query: 301 LHAARLKSAGL-------PCLSEASQA-----------KLFASEMAEKVCSQAVQIHGGY 342 A L C EA +A K+ ASE+ + + VQIHGGY Sbjct: 320 YRTAGLMEEACQDLDVTGDCRKEAGKAIEEYAIECSLNKVLASEVLDLAVDEGVQIHGGY 379 Query: 343 GYLEDYPVERYYRDARITQIYEGSSEIQRLLIARELANYAL 383 G++ +YP+ER YRD+RI +++EG++EI RLL+ L A+ Sbjct: 380 GFIAEYPIERMYRDSRINRLFEGTNEINRLLVPGTLLKRAM 420 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: 467 Number of extensions: 18 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 591 Length adjustment: 33 Effective length of query: 350 Effective length of database: 558 Effective search space: 195300 Effective search space used: 195300 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: 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