Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__PV4:5208388 Length = 391 Score = 201 bits (510), Expect = 4e-56 Identities = 131/379 (34%), Positives = 198/379 (52%), Gaps = 17/379 (4%) Query: 14 LGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAM 73 L ED +RD V D+AQ ++ R ++++ F ++ ++G+LG+LG T+PE YG A Sbjct: 18 LSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGELGLLGATLPEAYGCANA 77 Query: 74 GYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALA 133 Y+++ + EI R + + S+L ++ I GNE Q+ KYL KL +GE VG Sbjct: 78 NYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQRQKYLPKLATGEWVGCFG 137 Query: 134 MSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAF 193 ++EP GSD MK +AE G Y LNG+KMWITN P AD VV+AK + + F Sbjct: 138 LTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFVVWAKLDGV-----IRGF 192 Query: 194 LIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERA 253 ++EKGMKG S + K +R S TGE+V +VEV E +L + +G K L+ R Sbjct: 193 ILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEEALLPNV-EGLKGPFGCLNKARY 251 Query: 254 VLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAK 313 + G LG + Y DR QF + + QLIQ K+ADM T + G FA A Sbjct: 252 GIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEITTG-LFACLQAG 310 Query: 314 NL---DMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDA 370 L D L + + ++++ KA +A ++GGNG +E+ + R + Sbjct: 311 RLMDQDALPVEAISLIKRNSCG-------KALEIARTSRDMHGGNGISDEFHVIRHVMNL 363 Query: 371 KLYEIGAGTSEIRRMLIGR 389 + GT +I +++GR Sbjct: 364 EAVNTYEGTHDIHALILGR 382 Lambda K H 0.318 0.136 0.400 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: 372 Number of extensions: 17 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: 396 Length of database: 391 Length adjustment: 31 Effective length of query: 365 Effective length of database: 360 Effective search space: 131400 Effective search space used: 131400 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 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