Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS28375 RR42_RS28375 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS28375 Length = 402 Score = 355 bits (911), Expect = e-102 Identities = 189/410 (46%), Positives = 262/410 (63%), Gaps = 26/410 (6%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M L FS + AFR EVR F K +P+ ++K+ G + V W+RIL +GW W Sbjct: 1 MQLEFSAADDAFRQEVRAFVKARLPSDIKRKVELGLRLEHADYVTWFRILEARGWITPGW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P E+GG GWS +Q YIF+EE AP+ +A G+ M+GPV+ FG+ EQK R+LP I + Sbjct: 61 PVEHGGPGWSHLQRYIFDEETLLGGAPRIIASGIQMLGPVLIAFGTPEQKARYLPDIRHS 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKA--EKKGDKWIINGQKTWTTLAQHADWIFCLCRTDP- 177 + WW QGFSEPG+GSDLA+++T A E G +++NG K WT+ A +F L RTDP Sbjct: 121 NTWWAQGFSEPGAGSDLAAVRTTAVLEPDGRHFVVNGHKVWTSYAHWCSMMFALVRTDPD 180 Query: 178 AAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYA 237 AAK QEGISFIL+DM + G+ VRPI+ ++GG ++NE + D+V VP+ENLVG+ NKGW Y Sbjct: 181 AAKPQEGISFILIDMASPGVEVRPIRMLEGGTDLNECYLDNVRVPVENLVGEINKGWSYG 240 Query: 238 KFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALEL 297 K+LLG+ERTGIA +G K+++ R + LA + G +D + +LA EIEL ALE Sbjct: 241 KYLLGHERTGIAGIGSCKQQLARARTLADEQGLG-----DDAVLQCRLAQFEIELMALEY 295 Query: 298 TQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYD--------- 348 T LR++ D + P+ +S+LK++G+E++QA ELL+EV GP A P+D Sbjct: 296 TALRLLGDNQR--SRVPSVEASMLKVRGTELRQAIYELLVEVAGPHAVPFDEAAMLGAAG 353 Query: 349 ----VHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVL 394 D S T+ A +A Y ++RK+SIYGG NE+QRN+I KA L Sbjct: 354 YEQSTAADAASPPTL---AALAANYLDSRKLSIYGGVNEVQRNLISKAFL 400 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: 446 Number of extensions: 24 Number of successful extensions: 6 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: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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