Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 107 bits (268), Expect = 4e-28 Identities = 100/353 (28%), Positives = 175/353 (49%), Gaps = 48/353 (13%) Query: 61 PKEYGGTGW-----SSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLP 115 P+ YGG G +++ I L A A + G+ V I +GSEEQK+++LP Sbjct: 58 PEAYGGPGGDFGHEAAILIEIARANLSAWGAGHGIHSGI--VAHYILAYGSEEQKQKWLP 115 Query: 116 RIANVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRT 175 ++ + + +EPG+GSDL +KT+A K G+ + ++G K + T QHA+ I +T Sbjct: 116 KMVSGEMVGALAMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKT 175 Query: 176 DPAAKKQEGISFILVDMK-----TKGITVRPIQTIDGGH--EVNEVFFDDVEVPLENLVG 228 DP+A +G+S ++++ + ++G + + G H + +E+FFD+V +P ENL+G Sbjct: 176 DPSA-GAKGVSLVVLETEGAEGFSRGRNLHKV----GMHASDTSELFFDNVAIPPENLLG 230 Query: 229 QE-NKGWDYAKFLLGNERTGIA--RVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKL 285 E KG+ L ER IA VG + + R A + ++ G P+++ R KL Sbjct: 231 GEVGKGFYQMMTQLPQERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKL 290 Query: 286 AAVEIELKALELTQLRVVADE--GKHGKGKPN-PASSVLKIKGSEIQQATTELLMEVIGP 342 A + + T R +E +H +GK + +++ K ++ Q + +++ G Sbjct: 291 AECQ-----TKTTVARAFLNECMAEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGG 345 Query: 343 FA--APYDVHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393 + A YD IA + + R IYGG+NEI + +I +A+ Sbjct: 346 YGYMAEYD----------------IAQMWSDARVQRIYGGTNEIMKELIGRAL 382 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: 388 Number of extensions: 21 Number of successful extensions: 2 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: 382 Length adjustment: 30 Effective length of query: 366 Effective length of database: 352 Effective search space: 128832 Effective search space used: 128832 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