Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_2859 Ga0059261_2859 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Korea:Ga0059261_2859 Length = 392 Score = 332 bits (852), Expect = 9e-96 Identities = 179/398 (44%), Positives = 246/398 (61%), Gaps = 8/398 (2%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDL E A R +R F +D +P + + + GR +K + W RIL ++GW W Sbjct: 1 MDLTIPPEAEALRQAMRGFLRDQLPPELAEATLYGRKLSKGDHQRWQRILERQGWLAPSW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P ++GGTGW ++ +I++EE A AP+ + ++GPVI FG+E QK+ LPRI + Sbjct: 61 PTQWGGTGWGPLERFIWDEESALAGAPRANIPSLDLLGPVIVEFGTEAQKRELLPRILSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 +DWWCQGFSEP +GSDLA+L+ +A + GD +I+NG K WT+ A A+ IFCL RT Sbjct: 121 EDWWCQGFSEPQAGSDLAALQMRAVRDGDDYIVNGTKLWTSWAHMANKIFCLVRTSADGP 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 KQ GISF+L+DM+ G+T+ PI T+ G H VNEV DV VP+ NL+GQE W KFL Sbjct: 181 KQAGISFLLIDMEQPGVTISPILTLGGMHAVNEVQITDVRVPVANLLGQEGDAWTITKFL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 LG+ER A +G S R+++ ++ GG P+ +DP ++A VE +L AL T Sbjct: 241 LGHERLVGAGIGPSMALSRQLRGALGRIGPGGAPLGDDPVLAQRVAEVETDLLALRYTAY 300 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEV--IGPFAAPYDVHGDDDSNET 358 RV+ADE GK P P SVLKI+G E+QQA TELLMEV I P V E Sbjct: 301 RVLADE-LSGKA-PGPEVSVLKIRGGEVQQALTELLMEVGEIVSLTHPLTVSEGVVPIE- 357 Query: 359 MDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 +A +A +F+ RK++IYGGS+EIQRNII + +L + Sbjct: 358 ---SAYMAQQHFDRRKLTIYGGSSEIQRNIIARRLLNV 392 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: 437 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 365 Effective length of database: 361 Effective search space: 131765 Effective search space used: 131765 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