Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate WP_028314452.1 G491_RS0109680 KR domain-containing protein
Query= SwissProt::Q9NKW1 (441 letters) >NCBI__GCF_000429905.1:WP_028314452.1 Length = 910 Score = 331 bits (848), Expect = 7e-95 Identities = 193/432 (44%), Positives = 263/432 (60%), Gaps = 34/432 (7%) Query: 3 LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKA-ADKVVEEIK 61 +NF D+V ++TGAGGG+G+ YALE A RG KVVVNDLGG+ G G S + AD VVEEIK Sbjct: 492 INFNDRVAVITGAGGGLGRTYALELASRGCKVVVNDLGGARDGSGGGSASPADNVVEEIK 551 Query: 62 AAGGTAVANYDSV---EDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVY 118 GG AVANYD+V E G I+Q+A+D+FG +DI+INNAGILRD SF KM +W+ V Sbjct: 552 EMGGEAVANYDNVATPEGGAAIIQSAIDAFGRIDIVINNAGILRDKSFLKMEPENWNAVM 611 Query: 119 RVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178 VH GAY +++ A++ M+++ FGRIIMT+SAAGLYGNFGQ NY + KMALVG NTL Sbjct: 612 AVHLHGAYNVTKPAFSIMKQQGFGRIIMTTSAAGLYGNFGQTNYSAAKMALVGFMNTLKL 671 Query: 179 EGKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVG 238 EG NI NT+AP+AASRLTE +MPPEI +MKP+++ P+VLYL +D E+G +F G Sbjct: 672 EGAKYNIKVNTVAPLAASRLTEDIMPPEIFAKMKPEFVSPMVLYLASEDCKESGQIFNAG 731 Query: 239 AGWVSKVRLQRSAGVYMKD----LTPEKIKDNWAQIESFDNPSYPTSASESVSGILAAVN 294 G+ ++ + V + + T E I DNW I S + A E L +N Sbjct: 732 MGYFNRAAVMTGPSVQLGEGDTPPTLEDIADNWEAINSME------GAKE-----LNDLN 780 Query: 295 SKPADGESVLVRPPKVAVPKALAATPSGSVVVDGYNASKIFTTIQGNIGAKGAELVKKIN 354 + D ++ PP P A AA P+ + + IF + A AE ++ Sbjct: 781 TAMFD----MLSPP---APAAEAAAPAAGGEI---KPADIFAGMADTFNADKAE---GVD 827 Query: 355 GIYLINIKKGTNTQAWALDLKNGSGSIVVGAGSTKPNVTITVSDEDFVDIMTGKLNAQSA 414 ++ NI G N W + +K+ + ++ G K TI + D DFV +++G LN +A Sbjct: 828 VVFQFNI-SGGNGGEWNVTVKDKTCTVAEGKAG-KATCTIIMEDADFVGMISGTLNPMTA 885 Query: 415 FTKGKLKISGNM 426 F GKLKI G++ Sbjct: 886 FNSGKLKIEGDV 897 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: 932 Number of extensions: 57 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: 441 Length of database: 910 Length adjustment: 38 Effective length of query: 403 Effective length of database: 872 Effective search space: 351416 Effective search space used: 351416 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: 54 (25.4 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