Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate Pf1N1B4_4011 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4011 Length = 266 Score = 160 bits (404), Expect = 3e-44 Identities = 84/261 (32%), Positives = 137/261 (52%), Gaps = 1/261 (0%) Query: 11 IALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLIN 70 I LL+ I+ + V P YW++ S K+ L ++ + T +NY+ + +N Sbjct: 7 IPLLIYILFLLV-PIYWLLNMSFKSNTEILGGLTLFPQDFTFANYKVIFTDPSWYTGYLN 65 Query: 71 SLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNL 130 SL T ++L + +PAA+A +R+ F G K L+FW +TNRM P V LPFF + ++ Sbjct: 66 SLYYVSLNTVISLSVALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFLLPFFQLYSSI 125 Query: 131 GLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAM 190 GL D HI + L + FN+P+ +WI+ G+P ++DE A ++G S KI +PL Sbjct: 126 GLFDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYVDGYSFPKFFVKIFVPLIG 185 Query: 191 PGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIP 250 G+ V+A F F+FSW EL+ LT AK A+ + + +G + A L ++P Sbjct: 186 SGIGVTAFFCFMFSWVELLLARTLTSVNAKPIAAVMTRTVSASGIDWGVLAAAGVLTILP 245 Query: 251 VLIFALIASKQLVRGLTMGAV 271 ++ + +G +G V Sbjct: 246 GMLVIWFVRNHVAKGFALGRV 266 Lambda K H 0.331 0.143 0.431 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: 242 Number of extensions: 14 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: 272 Length of database: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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