Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate H281DRAFT_03746 H281DRAFT_03746 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__Burk376:H281DRAFT_03746 Length = 296 Score = 132 bits (333), Expect = 7e-36 Identities = 82/275 (29%), Positives = 144/275 (52%), Gaps = 8/275 (2%) Query: 14 IGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRTF 73 I P+++ + P+ +W SLH + R +F GL+N++T+ D F A RT Sbjct: 16 IAPSLVLALFIISYPIFNIVWQSLHEVSRFGAIR-DFTGLQNFYTIFGDPAFLAAARRTI 74 Query: 74 FLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQKF 133 + + + + +ALVL+Q + +AR ++LP + + + ++ + FN + Sbjct: 75 VWTVFVVGGTVLISVPVALVLNQDFYG--RGVARTIVMLPWSVSLTMTAVVWRWAFNDDY 132 Query: 134 GVVN---QLLG--GADINWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEEA 188 G+VN Q LG G I+W+ PE AF + I + PF +LL GL+ VPG++ EA Sbjct: 133 GMVNVTLQRLGLIGGPIHWLATPEFAFPVEIAVGILVSIPFTVTILLGGLSSVPGDIYEA 192 Query: 189 ARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISLM 248 AR++ S W R + LP L P + ++L F +++ +T+GGP +ST + Sbjct: 193 ARIDGASAWQQFRKLTLPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDNSTHILVTY 252 Query: 249 IQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRV 283 + +GFR G A+A ++I+L++ V + Y+R+ Sbjct: 253 LYELGFRLGRPGEAAAVSLIMLVMLFVFSMAYLRL 287 Lambda K H 0.329 0.144 0.440 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: 306 Number of extensions: 19 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: 288 Length of database: 296 Length adjustment: 26 Effective length of query: 262 Effective length of database: 270 Effective search space: 70740 Effective search space used: 70740 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