Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_052669986.1 NITAL_RS22860 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000969705.1:WP_052669986.1 Length = 392 Score = 463 bits (1191), Expect = e-135 Identities = 240/380 (63%), Positives = 287/380 (75%), Gaps = 6/380 (1%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 LTPE EE R+ V+EFA V+ P G+ E EFP +IV++MG+MGLFG+PF EE+GGMGG Sbjct: 19 LTPEQEEFRKVVKEFADTVIDPVAGELAEAGEFPTDIVKQMGQMGLFGIPFEEEWGGMGG 78 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124 D+L L +A+EEL RVD S+ ITLEAGV LGA+P+H+FGTD QK WLP LC GE + FG Sbjct: 79 DFLTLCLAIEELGRVDQSLGITLEAGVGLGAVPLHIFGTDEQKQRWLPELCRGERIAGFG 138 Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184 LTEP GGSD T T R E ++WVING+K FITN GT+++ +VTVTA TG + Sbjct: 139 LTEPHGGSDNWGTART-RAVEDGDDWVINGSKAFITNVGTEMSSIVTVTAWTGEQE---- 193 Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244 +S+IIVP+ TPG T+A PY KVGW+ASDTRELSF DVRVP NLLGE+G G QFL L Sbjct: 194 -LSAIIVPTATPGLTIAPPYRKVGWHASDTRELSFDDVRVPRDNLLGERGAGLKQFLYTL 252 Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGW 304 D+GRIAISALA GL QGCVDE V+YA ER AFGR IG +QA+ FKIADME+ A AR + Sbjct: 253 DDGRIAISALAVGLIQGCVDECVRYADEREAFGRPIGKHQAVAFKIADMEVAAQTARFMY 312 Query: 305 RDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKIL 364 +AA R G P+KKEAAIAKLYSS AV AREATQ+ GG GF E V R ++D+KIL Sbjct: 313 WNAAWRKAQGLPYKKEAAIAKLYSSEQAVTAAREATQVWGGMGFTTETRVGRFYQDAKIL 372 Query: 365 EIGEGTSEVQRMLIARELGL 384 EIGEGTSE+QR+LI+RELGL Sbjct: 373 EIGEGTSEIQRILISRELGL 392 Lambda K H 0.318 0.136 0.402 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: 530 Number of extensions: 20 Number of successful extensions: 3 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: 386 Length of database: 392 Length adjustment: 30 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 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 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