Align MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate HSERO_RS02190 HSERO_RS02190 sugar ABC transporter substrate-binding protein
Query= TCDB::O30491 (436 letters) >FitnessBrowser__HerbieS:HSERO_RS02190 Length = 451 Score = 527 bits (1357), Expect = e-154 Identities = 255/437 (58%), Positives = 315/437 (72%), Gaps = 1/437 (0%) Query: 1 MKFTAKALLACTCMTLSAVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60 ++FT A T TL IA++NN DMI +QKL+ FE +P+IKL WV + Sbjct: 15 VRFTLAAAAISTLFAAGLAQAEPVTLNIASINNPDMIELQKLAPAFEKANPDIKLRWVTM 74 Query: 61 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFPSVRD 120 EE+VLRQRLTTDIAT GQFD++TIG YEA +W KGWL PM LPA YD D+ VR+ Sbjct: 75 EESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLPADYDEADLIKPVRE 134 Query: 121 GLSVKGSLYALPFYAESSITYYRTDLFKDAGLSMPEHPTWSQIGEFAAKLTDKSKEQYGL 180 GLSV G LYALPFYAESS+TYYR DLF+ L+MP+ PTW +I + AA+L D +K YG+ Sbjct: 135 GLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKLAAQLHDPAKGVYGI 194 Query: 181 CLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGPPGAS 240 CLRG+AGWGENMA+ITT+AN +G RWFDE+WQP+ + PEWK ++ FYVD M+K GPPGAS Sbjct: 195 CLRGRAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAFYVDLMRKYGPPGAS 254 Query: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTSWLYS 300 SNGFNENL LF+SGKC +WVDA+VA + SKVAD F +P + TDKG+ WL+ Sbjct: 255 SNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPSPMQVTDKGSHWLWI 314 Query: 301 WSLAIPTSSKAKDAAKVFTSWATSKEYGALVAKTDGVANVPPGTRKSTY-SDEYMKAAPF 359 WSLA+P SSK++DAAK F +WATSKEY LVAK G A VPPGTR STY S EY K +PF Sbjct: 315 WSLAVPKSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRNSTYASAEYKKVSPF 374 Query: 360 AKVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDAALT 419 + L++++ AD KPT+KPVPY G+Q TIPEFQ+IGT G+ +GAL G+ T DAAL Sbjct: 375 SDFVLDAIQTADANKPTVKPVPYTGVQFATIPEFQSIGTVTGQAIAGALAGKTTSDAALD 434 Query: 420 AAQTTTEREMKRAGYPK 436 AAQ R M++ Y K Sbjct: 435 AAQAQAVRMMRQGRYIK 451 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: 624 Number of extensions: 25 Number of successful extensions: 2 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: 451 Length adjustment: 32 Effective length of query: 404 Effective length of database: 419 Effective search space: 169276 Effective search space used: 169276 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