Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 137 bits (346), Expect = 2e-37 Identities = 87/276 (31%), Positives = 135/276 (48%), Gaps = 7/276 (2%) Query: 11 FAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMG 70 F ++ P ++ + V + PL+ + S L ++G ENY + +D FW A+ Sbjct: 34 FLYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGFENYEKLWSDRKFWIALE 93 Query: 71 RTFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFN 130 TFF ++ Q LGLG+A++L+ K L + + LP A + L +FN Sbjct: 94 NTFFWTFWSIFFQFFLGLGLAMLLNTQFFG--KKLFQALVFLPWAVPTFLSALTWAWLFN 151 Query: 131 QKFGVVNQLLGGADI-----NWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEV 185 G + L + N +GDP+ A I ++W PF A+ LLA L +PGE+ Sbjct: 152 PVIGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGEL 211 Query: 186 EEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFI 245 EAA ++ + W + LPFL P + ++LRT D++F +T GGP +ST+ + Sbjct: 212 YEAAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTGGGPANSTQIL 271 Query: 246 SLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYI 281 S I FR D G AS A+ LLII + A I + Sbjct: 272 STYIFTTAFRKLDFGYASTIAVALLIILLAYAVILL 307 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: 313 Number of extensions: 13 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: 288 Length of database: 316 Length adjustment: 27 Effective length of query: 261 Effective length of database: 289 Effective search space: 75429 Effective search space used: 75429 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