Align MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF2258 PS417_11515 sugar ABC transporter substrate-binding protein
Query= TCDB::O30491 (436 letters) >FitnessBrowser__WCS417:GFF2258 Length = 436 Score = 664 bits (1714), Expect = 0.0 Identities = 319/431 (74%), Positives = 360/431 (83%) Query: 6 KALLACTCMTLSAVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVLEENVL 65 +AL + + L+ S A T+TIATVNNSDMIRMQ+LSK FE +HP+IKLNWVVLEENVL Sbjct: 6 QALFLLSGLALAIPSHAADTVTIATVNNSDMIRMQRLSKVFEEQHPDIKLNWVVLEENVL 65 Query: 66 RQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFPSVRDGLSVK 125 RQRLTTDIATQGGQFDVLTIG YE LWGAK WLEP+ LP YD DD+FPSVR GLSV Sbjct: 66 RQRLTTDIATQGGQFDVLTIGTYETPLWGAKHWLEPLTQLPPDYDADDIFPSVRQGLSVN 125 Query: 126 GSLYALPFYAESSITYYRTDLFKDAGLSMPEHPTWSQIGEFAAKLTDKSKEQYGLCLRGK 185 +LYALPFY ES++TYYRTDLFK AGLSMP HPTWSQ+GEFAAKLT K K QYG+CLRGK Sbjct: 126 NTLYALPFYGESTVTYYRTDLFKQAGLSMPAHPTWSQLGEFAAKLTAKDKGQYGMCLRGK 185 Query: 186 AGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGPPGASSNGFN 245 AGWGEN+AL++T+AN +GARWFDE+W+PE PEW A NFYV+ +K+ GPPG SSNGFN Sbjct: 186 AGWGENIALLSTMANAFGARWFDEQWKPELTSPEWTAAANFYVNTLKQYGPPGVSSNGFN 245 Query: 246 ENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTSWLYSWSLAI 305 E LALFNSGKCAIWVDASVAGSF TDK+QSKVAD VGF AP E TDKG+SWLY+WSLAI Sbjct: 246 ETLALFNSGKCAIWVDASVAGSFTTDKSQSKVADSVGFAAAPTEVTDKGSSWLYAWSLAI 305 Query: 306 PTSSKAKDAAKVFTSWATSKEYGALVAKTDGVANVPPGTRKSTYSDEYMKAAPFAKVTLE 365 P +SK KDAAK F SWATSK+Y LVA +G+ NVPPGTR+STYS+ Y+KAAPFA+VTLE Sbjct: 306 PATSKHKDAAKAFISWATSKDYIQLVADKEGITNVPPGTRQSTYSEAYLKAAPFAQVTLE 365 Query: 366 SLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDAALTAAQTTT 425 +K ADP P+ KPVPY+GIQ VTIPEFQAIGT VGK FS ALTG +VD AL AQ+TT Sbjct: 366 MMKHADPAHPSAKPVPYVGIQYVTIPEFQAIGTSVGKLFSAALTGGMSVDQALLDAQSTT 425 Query: 426 EREMKRAGYPK 436 EREMKRAGYPK Sbjct: 426 EREMKRAGYPK 436 Lambda K H 0.315 0.130 0.393 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: 715 Number of extensions: 17 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: 436 Length of database: 436 Length adjustment: 32 Effective length of query: 404 Effective length of database: 404 Effective search space: 163216 Effective search space used: 163216 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: 51 (24.3 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