Align MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Pf1N1B4_4850 Various polyols ABC transporter, periplasmic substrate-binding protein
Query= TCDB::O30491 (436 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4850 Length = 440 Score = 795 bits (2054), Expect = 0.0 Identities = 385/436 (88%), Positives = 414/436 (94%) Query: 1 MKFTAKALLACTCMTLSAVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60 M+ + KALLA TCMTLS+VSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL Sbjct: 1 MQPSVKALLALTCMTLSSVSLGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVL 60 Query: 61 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFPSVRD 120 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASY LDDVFPSVR+ Sbjct: 61 EENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYALDDVFPSVRE 120 Query: 121 GLSVKGSLYALPFYAESSITYYRTDLFKDAGLSMPEHPTWSQIGEFAAKLTDKSKEQYGL 180 GLSVKG+LYALPFYAESSITYYRTDLFKDAGL+MPE PTW+QI EFA+KLT+K KEQYG+ Sbjct: 121 GLSVKGTLYALPFYAESSITYYRTDLFKDAGLTMPERPTWTQISEFASKLTNKDKEQYGI 180 Query: 181 CLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGPPGAS 240 CLRGKAGWGENMALITT+AN YGARWFDE+W+PEF GPEWK+ALNFYVD MKKSGPPGAS Sbjct: 181 CLRGKAGWGENMALITTVANAYGARWFDEQWKPEFIGPEWKNALNFYVDTMKKSGPPGAS 240 Query: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTSWLYS 300 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKV+DHVGFT+APHE TDKG++WLYS Sbjct: 241 SNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVSDHVGFTYAPHETTDKGSAWLYS 300 Query: 301 WSLAIPTSSKAKDAAKVFTSWATSKEYGALVAKTDGVANVPPGTRKSTYSDEYMKAAPFA 360 W+LAIPTSSKAKDAAK F++WATSKEYGALVA+ DG+ANVPPGTR STY++ YM AAPFA Sbjct: 301 WALAIPTSSKAKDAAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYTEAYMNAAPFA 360 Query: 361 KVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVDAALTA 420 KVTLESLK ADP+KP+LKPVPYIGIQLVTIPEFQA+GTQVGK FS AL GQ TVD ALTA Sbjct: 361 KVTLESLKAADPSKPSLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALTA 420 Query: 421 AQTTTEREMKRAGYPK 436 AQ+TTEREMKRAGYPK Sbjct: 421 AQSTTEREMKRAGYPK 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: 790 Number of extensions: 18 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: 440 Length adjustment: 32 Effective length of query: 404 Effective length of database: 408 Effective search space: 164832 Effective search space used: 164832 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