Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_012113725.1 XAUT_RS08535 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_000017645.1:WP_012113725.1 Length = 396 Score = 355 bits (910), Expect = e-102 Identities = 185/399 (46%), Positives = 256/399 (64%), Gaps = 6/399 (1%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MD FS E AFR EVR F + N+PA ++ G H ++ +M W IL+ KGWA HW Sbjct: 1 MDTFFSDAEQAFRAEVRAFIRANLPADLAARVRAGIHLSRADMARWNAILDAKGWAAHHW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P+ YGG GW+ +Q ++F E A AP FGV +VGP +YTFGS+ QK+ +LP I + Sbjct: 61 PQTYGGPGWTPIQRFLFEAECADADAPPLSVFGVYLVGPTLYTFGSQAQKEAYLPGIRSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 +WCQG+SEP +GSDLASLKT A K ++I+G K WTT AD++ CL RT+P AK Sbjct: 121 ATFWCQGYSEPNAGSDLASLKTTARKVEGGYVIDGAKAWTTEGHFADYMICLARTNPQAK 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 Q G+S +VDM KG++++P+ TIDG H VN F D V VP + L+G+ +KGW YAKFL Sbjct: 181 PQAGLSLFIVDMTAKGVSLQPVITIDGAHSVNTTFLDAVFVPDDALIGEIDKGWTYAKFL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVES-GGKPVIEDPKFRDKLAAVEIELKALELTQ 299 L +ERT A+V S+ R+K+LA Q+ G V++DP F+ + AA+++EL ALE+T Sbjct: 241 LSHERTNNAQVHRSRREFTRLKELARQMSGPAGGSVLDDPVFQRRFAALDVELSALEVTV 300 Query: 300 LRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHG--DDDSNE 357 LRV+AD+ G+ +P P +S+LK+ GSE+QQ +EL MEV+G HG D ++ Sbjct: 301 LRVLADQ-TDGR-EPGPEASILKVIGSELQQRISELAMEVLGEEGIRQS-HGEVDGEAGA 357 Query: 358 TMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 A A + R V+IY G+NEIQ+ II + VLG+ Sbjct: 358 AATQAAGWAERHLFRRVVTIYAGANEIQKTIIARTVLGM 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: 397 Number of extensions: 17 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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 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