Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate BPHYT_RS29180 BPHYT_RS29180 sugar ABC transporter permease
Query= reanno::WCS417:GFF4322 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS29180 Length = 306 Score = 283 bits (723), Expect = 4e-81 Identities = 137/284 (48%), Positives = 195/284 (68%), Gaps = 9/284 (3%) Query: 7 KPAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKA 66 + A + +R+ +YA L+ A L +L+PL VML+TS K +I GNLL++PT T W A Sbjct: 23 RTAFTPARLGVYAFLLTAALFFLLPLYVMLVTSVKPMNEIRLGNLLAFPTHFTLSAWSAA 82 Query: 67 WAT---------VDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFG 117 W + + FWNS++I VP+ ++S AIGA+NGY LSFWR +G+ L FG+LL G Sbjct: 83 WQSACTGLDCNGIQVGFWNSVRIVVPSTILSIAIGAVNGYALSFWRPRGAGLLFGVLLMG 142 Query: 118 CFLPFQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAAR 177 F+P Q ++ P L + L S+ G+V +H ++G+ TL FRNYYVSIP L KAAR Sbjct: 143 AFIPVQVMVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYVSIPQELFKAAR 202 Query: 178 LDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVN 237 +DG GF+ IF Q++LPMSTPII+V +I Q T IWNDF+ G+VF+ + P+TV LNN++N Sbjct: 203 IDGGGFWRIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNNIIN 262 Query: 238 TSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281 T+TG + YNV+MAA ++ + L VY ++G++FVRG+ +GAVKG Sbjct: 263 TTTGERLYNVNMAATILTSMVPLAVYFVSGRWFVRGIASGAVKG 306 Lambda K H 0.328 0.141 0.435 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: 262 Number of extensions: 12 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: 281 Length of database: 306 Length adjustment: 26 Effective length of query: 255 Effective length of database: 280 Effective search space: 71400 Effective search space used: 71400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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