Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF1190 PGA1_c12060 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Phaeo:GFF1190 Length = 383 Score = 100 bits (248), Expect = 9e-26 Identities = 96/347 (27%), Positives = 166/347 (47%), Gaps = 38/347 (10%) Query: 61 PKEYGGTGWS-SVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIAN 119 P+EYGG G + I E +A A +V + ++G+EEQK+R+LP++ Sbjct: 61 PEEYGGVGGDFGHEAAILIEGSRANLASWGHGIHSGIVAHYVLSYGTEEQKQRWLPKMIT 120 Query: 120 VDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAA 179 + +EP +GSD+ +KTKA K G+ + ++GQKT+ T QHA+ I +TDP + Sbjct: 121 GELVGALAMTEPSTGSDVQRIKTKAVKDGNAYRLSGQKTFITNGQHANLILVAAKTDP-S 179 Query: 180 KKQEGISFILV-----DMKTKGITVRPIQTIDGGH--EVNEVFFDDVEVPLENLV-GQEN 231 + +GIS + V D ++G + I G H + +E+FFD+VE+ EN++ G E Sbjct: 180 QGSKGISLVAVETDGADGFSRGRNLDKI----GLHAADTSELFFDNVEIAPENILGGTEG 235 Query: 232 KGWDYAKFLLGNERTGIA--RVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVE 289 +G+ L ER IA VG + + R + E+ G P+ + R KL + Sbjct: 236 QGFYQMMQQLPQERLIIACGAVGAMEGAVERTITYCKEREAFGGPLTQFQNTRFKLVECQ 295 Query: 290 IELKALELTQLRVVADE--GKHGKGKPN-PASSVLKIKGSEIQQATTELLMEVIGPFAAP 346 + K R DE +H +GK +++ K ++ Q + +++ G + Sbjct: 296 TKTKV-----ARAFLDECMVEHLQGKLTVEKAAMAKYWITDTQGDVLDECVQLHGGYGFM 350 Query: 347 YDVHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393 + +A + + R IYGG+NEI + +I +++ Sbjct: 351 QEY--------------AVAEMWTDARVQRIYGGTNEIMKELIARSL 383 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: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 396 Length of database: 383 Length adjustment: 30 Effective length of query: 366 Effective length of database: 353 Effective search space: 129198 Effective search space used: 129198 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