Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate Pf1N1B4_4011 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4011 Length = 266 Score = 142 bits (358), Expect = 8e-39 Identities = 84/259 (32%), Positives = 133/259 (51%), Gaps = 4/259 (1%) Query: 17 VIILVAVFPFYYAILTSLKSGTALFR-IDYWPTDISLANYAGIFSHGTFVRNLGNSLLVA 75 + IL + P Y+ + S KS T + + +P D + ANY IF+ ++ NSL Sbjct: 11 IYILFLLVPIYWLLNMSFKSNTEILGGLTLFPQDFTFANYKVIFTDPSWYTGYLNSLYYV 70 Query: 76 TLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRFVGIFNT 135 +L ISL +A+ AAYA +R RF G L +L+ M P L F+L +G+F+T Sbjct: 71 SLNTVISLSVALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFLLPFFQLYSSIGLFDT 130 Query: 136 PLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLMWPALVT 195 +A+ ++ +F +P VW+L FM +P EI+E A VDG S ++F+PL+ + Sbjct: 131 HIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYVDGYSFPKFFVKIFVPLIGSGIGV 190 Query: 196 TGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVIVTVPLV 255 T F+ +W E L A T TS N + P+A + S I WG + AA V+ +P + Sbjct: 191 TAFFCFMFSWVELLLARTLTSVNAK---PIAAVMTRTVSASGIDWGVLAAAGVLTILPGM 247 Query: 256 VLVLIFQRRIISGLTAGGV 274 +++ + + G G V Sbjct: 248 LVIWFVRNHVAKGFALGRV 266 Lambda K H 0.332 0.143 0.426 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: 179 Number of extensions: 10 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: 276 Length of database: 266 Length adjustment: 25 Effective length of query: 251 Effective length of database: 241 Effective search space: 60491 Effective search space used: 60491 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