Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate RR42_RS18600 RR42_RS18600 ABC transporter permease
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__Cup4G11:RR42_RS18600 Length = 299 Score = 103 bits (256), Expect = 6e-27 Identities = 83/277 (29%), Positives = 134/277 (48%), Gaps = 11/277 (3%) Query: 13 FIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMGRT 72 F+ P + L + PL +W L F N E+IGL NY + D + A+ T Sbjct: 16 FMLPTALLLLVFLTYPLGLGVW--LGFTNTKIGGTGEWIGLSNYSYLAGDSLTQLALFNT 73 Query: 73 FFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFNQK 132 F A ++ ALGL +AL+L++ K+ R ++LP A+ L +++ + Sbjct: 74 IFYTVVASVVKFALGLWLALLLNKN--LPFKSFFRAIVLLPWIVPTALSALAFWWIYDAQ 131 Query: 133 FGVVNQLL---GGAD--INWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEVEE 187 F +++ L G D I+++GDP A I +VW+ PFVA+ LLAGL + + E Sbjct: 132 FSIISWTLVKLGLIDRYIDFLGDPWLARFSTIAANVWRGIPFVAISLLAGLQTISPTLYE 191 Query: 188 AARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFISL 247 AA ++ + W RYV LP L P + V+ T F +++ LTRGGP ++T ++ Sbjct: 192 AASIDGVTPWQQFRYVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGGPLNATHLMAT 251 Query: 248 MIQRVGFRGFDQGLASAQAIILLIITIVLAQIYIRVF 284 + + G L AI +++ +LA I F Sbjct: 252 LSFQRAIPG--GSLGEGAAIATMMVPFLLAAILFSYF 286 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: 292 Number of extensions: 23 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: 299 Length adjustment: 26 Effective length of query: 262 Effective length of database: 273 Effective search space: 71526 Effective search space used: 71526 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