Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate GFF4579 PS417_23435 serine/threonine protein kinase
Query= SwissProt::Q9NKW1 (441 letters) >FitnessBrowser__WCS417:GFF4579 Length = 303 Score = 336 bits (862), Expect = 5e-97 Identities = 157/293 (53%), Positives = 219/293 (74%), Gaps = 3/293 (1%) Query: 2 ALNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIK 61 ++ F+DKVVIVTGAGGG+G+ +AL FAK GAKV+VNDLGGS G+G+S+ AAD+VV EI+ Sbjct: 4 SVQFQDKVVIVTGAGGGLGRAHALLFAKHGAKVLVNDLGGSTQGEGASASAADRVVAEIR 63 Query: 62 AAGGTAVANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVH 121 AGG A AN+DSV DG++IVQ A+D+FG +D+++NNAGILRD +F KM D DWDLVYRVH Sbjct: 64 EAGGIAEANHDSVTDGDRIVQNALDAFGRIDVVVNNAGILRDKTFHKMDDSDWDLVYRVH 123 Query: 122 AKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGK 181 +GAYK++RAAW H+RE+ +GR+I T+S +G+YGNFGQ+NYG K+ L GL+ TLA EG+ Sbjct: 124 VEGAYKVTRAAWPHLREQGYGRVIFTASTSGIYGNFGQSNYGMAKLGLYGLTRTLALEGR 183 Query: 182 SKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVGAGW 241 NI N IAP +R+TE ++PP++ E++KP+ + PLV+YL + ET G+FEVG GW Sbjct: 184 KNNILVNAIAPTGGTRMTEGLIPPQVFERLKPELVSPLVVYLGSEACQETSGLFEVGGGW 243 Query: 242 VSKVRLQRSAGVYM---KDLTPEKIKDNWAQIESFDNPSYPTSASESVSGILA 291 + K R +RS GV +P+ + +W QI F+ ++P E++ ++A Sbjct: 244 IGKTRWERSLGVGFDPEAGFSPDDVAAHWQQICDFEGAAHPKDNIEALKEMMA 296 Lambda K H 0.313 0.131 0.371 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: 385 Number of extensions: 21 Number of successful extensions: 1 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: 441 Length of database: 303 Length adjustment: 30 Effective length of query: 411 Effective length of database: 273 Effective search space: 112203 Effective search space used: 112203 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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