Align ABC transporter for D-sorbitol, periplasmic substrate-binding component (characterized)
to candidate GFF2258 PS417_11515 sugar ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_1963 (436 letters) >FitnessBrowser__WCS417:GFF2258 Length = 436 Score = 764 bits (1974), Expect = 0.0 Identities = 368/434 (84%), Positives = 401/434 (92%) Query: 2 KITNALILSTGLSFALASHAAETLTIATVNNGDMIRMQRLSKVFEQQHPDIKLSWVVLEE 61 K+ AL L +GL+ A+ SHAA+T+TIATVNN DMIRMQRLSKVFE+QHPDIKL+WVVLEE Sbjct: 3 KLPQALFLLSGLALAIPSHAADTVTIATVNNSDMIRMQRLSKVFEEQHPDIKLNWVVLEE 62 Query: 62 NVLRQRLTTDIATQGGQFDVLTIGTYETPMWGAKNWLEPMKDLPAGYDVDDIFPAVRQGL 121 NVLRQRLTTDIATQGGQFDVLTIGTYETP+WGAK+WLEP+ LP YD DDIFP+VRQGL Sbjct: 63 NVLRQRLTTDIATQGGQFDVLTIGTYETPLWGAKHWLEPLTQLPPDYDADDIFPSVRQGL 122 Query: 122 SVNDTLYALPFYGESTITYYRTDLFKAAGLTMPAQPTWSQLGEFAAKLNDPSKDQYGMCL 181 SVN+TLYALPFYGEST+TYYRTDLFK AGL+MPA PTWSQLGEFAAKL K QYGMCL Sbjct: 123 SVNNTLYALPFYGESTVTYYRTDLFKQAGLSMPAHPTWSQLGEFAAKLTAKDKGQYGMCL 182 Query: 182 RGKAGWGENMALLTTMANAFGARWFDEKWQPELNGPEWKAAATFYVDTLKKYGPPGVSSN 241 RGKAGWGEN+ALL+TMANAFGARWFDE+W+PEL PEW AAA FYV+TLK+YGPPGVSSN Sbjct: 183 RGKAGWGENIALLSTMANAFGARWFDEQWKPELTSPEWTAAANFYVNTLKQYGPPGVSSN 242 Query: 242 GFNETLALFNSGKCAIWVDASVAGSFTTDKEQSRVVDSVGFAPAPTEVTDKGSSWLYAWS 301 GFNETLALFNSGKCAIWVDASVAGSFTTDK QS+V DSVGFA APTEVTDKGSSWLYAWS Sbjct: 243 GFNETLALFNSGKCAIWVDASVAGSFTTDKSQSKVADSVGFAAAPTEVTDKGSSWLYAWS 302 Query: 302 LAIPATSKHKEAAKSFVTWATSKEYIQLVTDKDGITNVPPGTRISTYSDAYLKAAPFAQV 361 LAIPATSKHK+AAK+F++WATSK+YIQLV DK+GITNVPPGTR STYS+AYLKAAPFAQV Sbjct: 303 LAIPATSKHKDAAKAFISWATSKDYIQLVADKEGITNVPPGTRQSTYSEAYLKAAPFAQV 362 Query: 362 TLQMMKHADPSQPSAKPVPYVGIQYVVIPEFQSIGTSVGKLFSAALTGQMSVEQALASAQ 421 TL+MMKHADP+ PSAKPVPYVGIQYV IPEFQ+IGTSVGKLFSAALTG MSV+QAL AQ Sbjct: 363 TLEMMKHADPAHPSAKPVPYVGIQYVTIPEFQAIGTSVGKLFSAALTGGMSVDQALLDAQ 422 Query: 422 STTEREMKRAGYPK 435 STTEREMKRAGYPK Sbjct: 423 STTEREMKRAGYPK 436 Lambda K H 0.315 0.130 0.391 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: 771 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: 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