Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein (characterized)
to candidate BPHYT_RS16115 BPHYT_RS16115 sugar ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF2493 (440 letters) >FitnessBrowser__BFirm:BPHYT_RS16115 Length = 440 Score = 549 bits (1414), Expect = e-161 Identities = 269/441 (60%), Positives = 325/441 (73%), Gaps = 6/441 (1%) Query: 1 MKFTAKALLASTCMMTCMTLSAVSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLN 60 +K T KA+ A + C LSA A T+TIAT+NN DMI ++KLS FE +P+IKLN Sbjct: 5 LKSTLKAVSAGA--VACFALSA---SAATVTIATLNNPDMIELKKLSPEFEKANPDIKLN 59 Query: 61 WVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFP 120 WV+LEENVLRQR TTDI T GQFDV+TIG YE WG +GWL P+ +LPA YDL+DV Sbjct: 60 WVILEENVLRQRATTDITTGSGQFDVMTIGAYETPQWGKRGWLTPLTNLPADYDLNDVVK 119 Query: 121 SVRDGLSVKGSLYALPFYAESSITYYRTDLFKDAGLTMPEHPTWTQIGEFASKLTDKTKE 180 + RDGLS G LYALPFY ESS+TYYR DLF+ AGL MP+ PT+ QI +FA KLTDK Sbjct: 120 TARDGLSSGGQLYALPFYVESSMTYYRKDLFEKAGLKMPDQPTYDQIKQFADKLTDKANG 179 Query: 181 QYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGP 240 YG+CLRGKAGWGENMA TT+ N +G RWFDEKW + PEWK A+ FYVD +KK GP Sbjct: 180 IYGICLRGKAGWGENMAYGTTVVNTFGGRWFDEKWNAQLTSPEWKKAMTFYVDLLKKDGP 239 Query: 241 PGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTS 300 PGASSNGFNENL L +SGKCA+W+DA+VA + +K QS++AD VGF AP T KG+ Sbjct: 240 PGASSNGFNENLTLMSSGKCAMWIDATVAAGMLYNKQQSQIADKVGFAAAPVAVTPKGSH 299 Query: 301 WLYSWSLAIPTSSKAKDAAKVFTSWATSKEYGELVAKTDGIANVPPGTRKSTY-NDEYMK 359 WL++W+LAIP SSK DAAK F +WATSK+Y ELVAK +G A+VPPGTRKSTY EY + Sbjct: 300 WLWAWALAIPKSSKQADAAKKFITWATSKQYIELVAKDEGWASVPPGTRKSTYARAEYKQ 359 Query: 360 AAPFAKVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVD 419 AAPF L++++ ADP PTLKPVPY G+Q V IPEFQ+ GT VG+ SGA+ GQ T+D Sbjct: 360 AAPFGDFVLKAIETADPEHPTLKPVPYTGVQFVGIPEFQSFGTVVGQSISGAIAGQMTID 419 Query: 420 AALTAAQTTTEREMKRAGYPK 440 AL A T +R +K+AGY K Sbjct: 420 QALAAGNATADRAVKQAGYQK 440 Lambda K H 0.315 0.130 0.394 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: 627 Number of extensions: 20 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: 440 Length of database: 440 Length adjustment: 32 Effective length of query: 408 Effective length of database: 408 Effective search space: 166464 Effective search space used: 166464 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