Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF402 PGA1_c04130 putative acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Phaeo:GFF402 Length = 399 Score = 415 bits (1066), Expect = e-120 Identities = 208/400 (52%), Positives = 279/400 (69%), Gaps = 9/400 (2%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDLN+S E++AFR EVR F +P + GR KE W+ ILN++GW W Sbjct: 1 MDLNYSTEDVAFRAEVRAFLDAKLPQDLSDAVRLGRGLGKEGHDRWHSILNEQGWLAPTW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P+EYGG GW++VQ +IF EE A AP+ + FG++M+ PV+ FGS+EQ+ FLP+I + Sbjct: 61 PEEYGGCGWNAVQRHIFEEECCRAHAPRIVPFGLTMLAPVLQKFGSDEQRAYFLPKILSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 + WWCQG+SEPG+GSDLASL+T+A + GD +++NGQKTWTTL Q+A+WIFCL RTDP AK Sbjct: 121 EHWWCQGYSEPGAGSDLASLRTRAVRDGDHYVVNGQKTWTTLGQYANWIFCLVRTDPDAK 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 +QEGISF+L+DM T GI VRPI +DG HEVNEV+F DV VP+ENLVG+ENKGW YAK+L Sbjct: 181 QQEGISFLLIDMDTPGIEVRPIILLDGTHEVNEVWFTDVRVPVENLVGEENKGWTYAKYL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ERT IA VG S+ + +K+LA Q G+P+IE+P F +LA EI+L A+ T L Sbjct: 241 LTHERTNIAGVGFSQAGLEAVKRLARQQIHRGRPLIENPHFAARLARAEIDLMAMATTNL 300 Query: 301 RVV--ADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY---DVHGDDDS 355 R++ A +G+ P SS+LK+KG+EI+Q +L G +A P+ + GD+ + Sbjct: 301 RIISAAAQGQ----APGVESSMLKVKGTEIRQEINDLARRAAGVYALPFASEALAGDNSA 356 Query: 356 NETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLG 395 + + A YFNNRK+SI+GGSNEIQ+NII K LG Sbjct: 357 LAPPEGSDAAAAQYFNNRKLSIFGGSNEIQKNIIAKISLG 396 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: 433 Number of extensions: 14 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: 399 Length adjustment: 31 Effective length of query: 365 Effective length of database: 368 Effective search space: 134320 Effective search space used: 134320 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