Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate Pf6N2E2_2890 Glucose ABC transport system, inner membrane component 2
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2890 Length = 281 Score = 113 bits (283), Expect = 6e-30 Identities = 71/215 (33%), Positives = 108/215 (50%), Gaps = 9/215 (4%) Query: 167 FLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLY 226 F NS+ + VP+ +I I A Y L+ F G + +++ +P Q L+P Sbjct: 74 FWNSIKITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133 Query: 227 NGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFV 286 +G A T G+ H +GL RNY +P ++++AR+DGA F IF Sbjct: 134 GKMGL-----ASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFR 188 Query: 287 KIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGG--NWE 344 +IILP+S P + I+QF WND L +VF + D +T L NL+ + G + Sbjct: 189 RIILPMSTPIIMVCLIWQFTQIWNDFLFGVVF--SSGDSQPITVALNNLVNTSTGAKEYN 246 Query: 345 ILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 + A+A I + L+V+ +Y VRGL AG+VKG Sbjct: 247 VDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281 Lambda K H 0.324 0.139 0.418 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: 252 Number of extensions: 14 Number of successful extensions: 3 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: 380 Length of database: 281 Length adjustment: 28 Effective length of query: 352 Effective length of database: 253 Effective search space: 89056 Effective search space used: 89056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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