Align MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate AO353_25880 AO353_25880 sugar ABC transporter substrate-binding protein
Query= TCDB::O30491 (436 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25880 Length = 436 Score = 796 bits (2057), Expect = 0.0 Identities = 385/436 (88%), Positives = 409/436 (93%) Query: 1 MKFTAKALLACTCMTLSAVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60 MK T KALLACTCMTLS+VSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL Sbjct: 1 MKPTVKALLACTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60 Query: 61 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFPSVRD 120 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPA Y LDDVFPSVR+ Sbjct: 61 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPAGYALDDVFPSVRE 120 Query: 121 GLSVKGSLYALPFYAESSITYYRTDLFKDAGLSMPEHPTWSQIGEFAAKLTDKSKEQYGL 180 GLSVKG+LYALPFYAESS+TYYRTDLFKDAGL+MPEHPTW QIGEFA KL +EQYG+ Sbjct: 121 GLSVKGTLYALPFYAESSMTYYRTDLFKDAGLAMPEHPTWEQIGEFAGKLNKPDQEQYGI 180 Query: 181 CLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGPPGAS 240 CLRGKAGWGENMALITT+AN YGARWFDEKWQPEF+GPEWK+AL+FY D MKKSGPPGAS Sbjct: 181 CLRGKAGWGENMALITTIANAYGARWFDEKWQPEFSGPEWKNALSFYADTMKKSGPPGAS 240 Query: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTSWLYS 300 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKV++HVGFT+APH+ TDKG++WLYS Sbjct: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSEHVGFTYAPHQVTDKGSAWLYS 300 Query: 301 WSLAIPTSSKAKDAAKVFTSWATSKEYGALVAKTDGVANVPPGTRKSTYSDEYMKAAPFA 360 W+LAIPTSSKAKDAAK F++WATSKEYGALVA+ DG+ANVPPGTR STYS+ YM AAPFA Sbjct: 301 WALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYSEAYMNAAPFA 360 Query: 361 KVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDAALTA 420 KVTLESLKVADP KPTLKPVPYIGIQLVTIPEFQA+GTQVGK FS AL GQ TVD AL A Sbjct: 361 KVTLESLKVADPGKPTLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALAA 420 Query: 421 AQTTTEREMKRAGYPK 436 AQ TTEREMKRAGYPK Sbjct: 421 AQQTTEREMKRAGYPK 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: 811 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