Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_015947942.1 G491_RS0109685 KR domain-containing protein
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000429905.1:WP_015947942.1 Length = 703 Score = 323 bits (827), Expect = 1e-92 Identities = 185/431 (42%), Positives = 260/431 (60%), Gaps = 33/431 (7%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62 + + +V ++TGAG G+GK YALE AKRGAKVV+NDLGGS G G+SS AAD VV+EIKA Sbjct: 287 IRYDGRVAVITGAGAGLGKAYALELAKRGAKVVINDLGGSRDGTGASSSAADAVVDEIKA 346 Query: 63 AGGTAVANYDSV---EDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119 AGG AVANYD+V E G +++TA+D+FG VDI+INNAGILRD SF KM +W+ V Sbjct: 347 AGGEAVANYDNVATPEGGANVIKTAVDAFGKVDIVINNAGILRDKSFVKMEPENWNAVLN 406 Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQE 179 VH GAY +++AA+ M++ FGRI+MT+SAAGLYGNFGQ NY + KMALVG NTL E Sbjct: 407 VHLNGAYNVTKAAFPIMKQNGFGRIVMTTSAAGLYGNFGQTNYSAAKMALVGFMNTLKIE 466 Query: 180 GKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVGA 239 G +I NT+AP+AASRLTE +MP EI + KP+Y+VP+ LYLC + TG ++ VG Sbjct: 467 GNKYDIKVNTVAPLAASRLTEDIMPEEIFNKAKPEYVVPMTLYLCTDECDVTGRIYNVGM 526 Query: 240 GWVSKVRLQRSAGVYM---KDL-TPEKIKDNWAQIESFDNPSYPTSASESVSGILAAVNS 295 G+ ++ + G + D+ T + +K + A I S + + V ++ A + Sbjct: 527 GFFNRAAVVTGPGAVLGQGDDIPTCDDVKASMANIGSLKDGKEYFELNAQVGDVMMAFQA 586 Query: 296 KPADGESVLVRPPKVAVPKALAATPSGSVVVDGYNASKIFTTIQGNIGAKGAELVKKING 355 P+ G + P ATP+ + + + +T Q + A G ++V + Sbjct: 587 PPSGGAAAAAGP----------ATPADAFAM-------LESTFQPD-AADGVDVVFQ--- 625 Query: 356 IYLINIKKGTNTQAWALDLKNGSGSIVVGAGSTKPNVTITVSDEDFVDIMTGKLNAQSAF 415 Y I+ G W +K+ + + G KP I + D+DF+ + G LN A+ Sbjct: 626 -YSIS---GATGGEWNAVIKDKTCKVSEGK-HDKPTTVIIMEDKDFMAMTAGTLNPMQAY 680 Query: 416 TKGKLKISGNM 426 T GKLKI G++ Sbjct: 681 TSGKLKIEGDV 691 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: 818 Number of extensions: 39 Number of successful extensions: 3 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: 703 Length adjustment: 36 Effective length of query: 405 Effective length of database: 667 Effective search space: 270135 Effective search space used: 270135 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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