Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_085772269.1 B1812_RS14765 acyl-CoA dehydrogenase family protein
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_002117405.1:WP_085772269.1 Length = 557 Score = 229 bits (585), Expect = 1e-64 Identities = 140/384 (36%), Positives = 208/384 (54%), Gaps = 12/384 (3%) Query: 10 LGEEIDALRASVRRFASERIAPLADDADRSNAF-PMSLWREMGELGLLGITADEAHGGAG 68 L E ++A+R+ +R+FAS+ + P A + N + P+ + + ELG+ G+T E GG+G Sbjct: 172 LDETLEAIRSEMRKFASDNVTPFAQEWHAKNEYIPLEVISGLAELGVFGLTIPEEFGGSG 231 Query: 69 LGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGAL 128 +G +A CV EE+SRA VG S G S + I G AQK +YLPK+ +GE + Sbjct: 232 MGKIAMCVVSEELSRAYIGVG-SLGTRSEIAGELILVGGTKAQKEKYLPKIAAGEILPTA 290 Query: 129 AMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAA-GPRGIT 187 +EP GSD+ ++ +A + GD Y + G+K WIT+ ADV+ + +T+P G +G++ Sbjct: 291 VFTEPNNGSDLAGLRTRAVREGDVYKVTGNKTWITHPVRADVMTLLVRTNPEEKGYKGLS 350 Query: 188 AFLVEKA-------FPGFS-AGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGV-GEGVK 238 L EK FP G +++ LG RG E+ F E P EN+LGGV G G K Sbjct: 351 MLLAEKPRGTDENPFPAKGMTGGEIEVLGYRGMKEFEIGFDGFETPAENLLGGVEGNGFK 410 Query: 239 VLMSGLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMN 298 LM + R+ +A LG+ LD+ + Y ER QFG+P+ F + K+ M V ++ Sbjct: 411 QLMETFESARIQTAARALGVAQCALDLGLRYAKERIQFGKPLFSFPRIFDKIVAMAVEIH 470 Query: 299 AARAYVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLL 358 AR Y A D G+ +A L A A A A A+Q GGNG+ +YP R+L Sbjct: 471 VARQITYFSARQKDGGKRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYPVSRVL 530 Query: 359 RDAKLYEIGAGTSEIRRMLIGREL 382 DA++ I G +EI+ +I R L Sbjct: 531 CDARILNIFEGAAEIQAQVIARRL 554 Lambda K H 0.318 0.135 0.391 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: 388 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: 387 Length of database: 557 Length adjustment: 33 Effective length of query: 354 Effective length of database: 524 Effective search space: 185496 Effective search space used: 185496 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 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