Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS29935 RR42_RS29935 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS29935 Length = 393 Score = 409 bits (1052), Expect = e-119 Identities = 205/402 (50%), Positives = 284/402 (70%), Gaps = 16/402 (3%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDLNF++EE FR EV + ++P + K+ G ++ +M W++IL KKGW W Sbjct: 1 MDLNFTEEEQEFRKEVHAWIDAHLPKEISHKVHNGLQLSRTDMQRWHQILGKKGWLTYKW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P E+GGTGW+ VQ +IF EE A AP+ + +G MV PVI FG+ EQ+ RFLP I Sbjct: 61 PVEFGGTGWTPVQRHIFEEECALAGAPRLVPYGPVMVAPVIMAFGNAEQQARFLPGIVTG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 D WW QG+SEPGSGSDLASLKT+AE+KGDK+I+NGQK WTTLAQ+ +WIFCL RT+ K Sbjct: 121 DVWWSQGYSEPGSGSDLASLKTRAERKGDKYIVNGQKIWTTLAQYGEWIFCLVRTNTEGK 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 Q GISF+L+DM++ G+TVRPI+ +DG EVNEV+FD+VEVP+ENL+G+ENKGW YAK L Sbjct: 181 PQAGISFLLIDMRSPGVTVRPIKLLDGECEVNEVWFDNVEVPVENLIGEENKGWTYAKHL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ER+ IA VG +K +RR+K++AA + +++DP+F+D+++ +E+++ ALE+ L Sbjct: 241 LSHERSNIAEVGRAKRELRRLKRIAA-----AEGMMDDPRFKDEVSKLEVDIIALEMLVL 295 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY-------DVHGDD 353 RV++ E K GK P + +LKI+GSEIQQ +EL+M GP++ P+ + G+ Sbjct: 296 RVISAE-KSGK-NPLDIAGLLKIRGSEIQQRYSELMMLAAGPYSLPFIQDAMLTEWDGEF 353 Query: 354 DSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLG 395 E + A +A YFN RK +IYGGSNE+QRNI+ + VLG Sbjct: 354 PGGERRN--APLAATYFNLRKTTIYGGSNEVQRNIVSQVVLG 393 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: 484 Number of extensions: 18 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: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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