Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate PfGW456L13_2495 Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor (EC 1.3.99.13)
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2495 Length = 397 Score = 246 bits (628), Expect = 8e-70 Identities = 148/408 (36%), Positives = 214/408 (52%), Gaps = 31/408 (7%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEG----RHNTKEEMVEWYRILNKKGWA 56 M ++FS+++ FR EV + N+ + G H EE W R L + GW Sbjct: 1 MKISFSEQDERFRREVADWMSANLCGEFEALRFRGGPGDEHMFPEERKAWERKLAEGGWT 60 Query: 57 VTHWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLA-FGVSMVGPVIYTFGSEEQKKRFLP 115 W E+GG G S Q IFNEE A P + G + GP I FG+ EQ++RFLP Sbjct: 61 CVGWAPEHGGRGLSITQQVIFNEEYARAGGPGRMGHIGEGLAGPTIAAFGTVEQQQRFLP 120 Query: 116 RIANVDDWWCQGFSEPGSGSDLASLKTKA--EKKGDKWIINGQKTWTTLAQHADWIFCLC 173 I + +WCQG+SEPG+GSDLAS+KT+A ++ WIINGQK WT+LA +DW F + Sbjct: 121 GIVSGTSFWCQGYSEPGAGSDLASVKTRATLDEATGSWIINGQKVWTSLAHESDWCFVIA 180 Query: 174 RTDPAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKG 233 RT+P + G+SF+LV M ITVRPI+ + G E NEVFFDD N++G +G Sbjct: 181 RTEPGSVGHRGLSFLLVPMAQTEITVRPIEQLTGTSEFNEVFFDDARTDATNIIGAPGEG 240 Query: 234 WDYAKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELK 293 W A LLG ER G++ +G + + ++ A ++ G DP R +LA L+ Sbjct: 241 WKIAMALLGFER-GVSTLGQQMQFQNELNEIIAIAKTNGAD--RDPILRQRLAEAWSGLR 297 Query: 294 ALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGP-----FAAPYD 348 + LR+++ G +++ K+ S + +L M+V+G AAPY Sbjct: 298 IMRYNSLRMLSGS---QDGSLRKEATIYKLFWSTWHASLGKLAMDVLGAEAELLEAAPYQ 354 Query: 349 VHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 + ++ Y +R ++YGGSNEIQRNII + LG+ Sbjct: 355 L-------------TRLQSLYLFSRADTLYGGSNEIQRNIIAERALGM 389 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: 458 Number of extensions: 22 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: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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