Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF4161 Psest_4234 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__psRCH2:GFF4161 Length = 398 Score = 439 bits (1128), Expect = e-128 Identities = 215/400 (53%), Positives = 296/400 (74%), Gaps = 6/400 (1%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M++N++ EE+AFRDEVR F K +PA K+ G+H +K++ W +IL K+GW W Sbjct: 1 MNVNYTAEELAFRDEVRAFLKSELPADIAAKVKLGKHMSKQDHERWQQILVKRGWYAPGW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P E GGT W V+ +IF+EE A AP+ + FGV+MV PVI FG+++Q +LPRI + Sbjct: 61 PVELGGTTWGPVEKHIFDEECSAFGAPRTVPFGVNMVAPVIIKFGTQQQIDHYLPRILSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 +DWWCQG+SEPG+GSDLASLKT+A + GD +++NGQKTWTTL QHA+ IFCL RTDP A+ Sbjct: 121 EDWWCQGYSEPGAGSDLASLKTRAVRDGDHYVVNGQKTWTTLGQHANMIFCLVRTDPEAQ 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 +Q GISF+L+DMK+ GI+VRPI T+DG HEVNEVFFD+V VP+ENLVG+EN+GW AK+L Sbjct: 181 QQRGISFLLIDMKSPGISVRPIITLDGDHEVNEVFFDNVRVPVENLVGEENQGWTCAKYL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ERTG+A +G SK + +K++A + GKP++EDP FR ++A VE++L A+E++ L Sbjct: 241 LTHERTGLAGIGSSKAVLAHLKRIAMKEVCDGKPMLEDPLFRAQVAEVEMQLMAIEMSTL 300 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY---DVHGDDDSNE 357 R++A K G G P SS+LK+KG+EI+QA T LL +VIGP+A P+ ++ D D Sbjct: 301 RILA-AAKEG-GVPGAESSILKVKGTEIRQAITHLLRKVIGPYALPFLEEEMQLDYDGEL 358 Query: 358 T-MDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 D++A +A YFN RK+SI+GGSNEIQ+NI+ K +L L Sbjct: 359 LHADYSASLAGDYFNMRKLSIFGGSNEIQKNIVSKMILEL 398 Lambda K H 0.317 0.135 0.411 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: 461 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: 396 Length of database: 398 Length adjustment: 31 Effective length of query: 365 Effective length of database: 367 Effective search space: 133955 Effective search space used: 133955 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 (21.6 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