Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01883 CCNA_01883 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Caulo:CCNA_01883 Length = 390 Score = 344 bits (882), Expect = 3e-99 Identities = 177/398 (44%), Positives = 253/398 (63%), Gaps = 10/398 (2%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M+L+ + E+ AFRDEVR FF +NVP + ++ G E +W ++L +GW W Sbjct: 1 MNLDLTPEQSAFRDEVRAFFAENVPESFKSRVRAGMRLEPHEFTQWQKLLYARGWGAPSW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 PKEYGGTGW + YIF E A AP G+ ++GP+I+TFGS EQK ++LP I + Sbjct: 61 PKEYGGTGWDPTKLYIFETEASRADAPVQFHQGLELIGPIIFTFGSPEQKAKYLPAIVSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 DDWWCQG+SEP SGSDLASL T+A + G++++INGQK WT+ A A+ +F L RTDP A+ Sbjct: 121 DDWWCQGYSEPNSGSDLASLSTRAVRDGNEYVINGQKAWTSYAHVANRMFLLARTDPDAR 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 KQ GIS L+D+ T G+T+RP+ T+D H NEVF D+V VP L+G+E GW Y K L Sbjct: 181 KQAGISLFLIDIDTPGVTIRPVVTMDEIHHTNEVFLDNVRVPPSALLGEEGMGWSYGKVL 240 Query: 241 LGNERTGIARVGMSK--ERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELT 298 L ER G+ ++ +++R +++AA+ GG+ +++DP+ D+LA E+E+ ALE Sbjct: 241 LDRER-GVTAATTTRLAQQLRGARKVAAETMVGGRSLLDDPRVADRLAQFELEVMALEGM 299 Query: 299 QLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNET 358 +R +A E G+ P +S++KI+ SE+ Q TE +E+ G A + G ++ + Sbjct: 300 VMRTMA-EATSGQDS-GPRASMIKIRWSELLQQITEYWVELQGYDAMAFAPLGPFEAPDA 357 Query: 359 MDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 W A+ G +R SIYGGSNEIQRNII + LGL Sbjct: 358 --WAAK---GMIYSRVTSIYGGSNEIQRNIIARRALGL 390 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: 410 Number of extensions: 15 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: 390 Length adjustment: 31 Effective length of query: 365 Effective length of database: 359 Effective search space: 131035 Effective search space used: 131035 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