Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Phaeo:GFF3854 Length = 309 Score = 240 bits (612), Expect = 3e-68 Identities = 121/275 (44%), Positives = 184/275 (66%), Gaps = 11/275 (4%) Query: 5 LLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW-------- 56 +LYG LLL+A ++LLP+Y++V+T+LK I L ++ P ++ + AW Sbjct: 35 MLYGTLLLIALYYLLPLYVMVVTSLKGMPEIRLGNIFSPPVEITFQPWIKAWSEACTGIN 94 Query: 57 -EAFRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSIL 115 + F NS+ + V + LS + S+NGY LA W F+GS F +++ G FIPYQ++L Sbjct: 95 CDGLSRGFGNSIKILVPSVALSIAIASVNGYALANWRFKGSETFFTILIIGAFIPYQTML 154 Query: 116 IPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGI 175 P+ ++ + L GSL+GLVLVH I+G+PI+TL+FRNY+S +P+EL +AAR+DGAGF+GI Sbjct: 155 YPIVIILRELKLMGSLWGLVLVHSIFGMPILTLLFRNYFSSLPEELFKAARVDGAGFWGI 214 Query: 176 FRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAGG-EAVK-WN 233 + V++P+S+P FVV I Q T IWN+FLF V T+PE+ P+TV L + + VK +N Sbjct: 215 YLRVMVPMSIPIFVVAMILQVTGIWNDFLFGVIYTKPETYPMTVQLNNIVNSVQGVKEYN 274 Query: 234 LPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268 + MA +L L L++Y++ G+ F+RG+ AG+VKG Sbjct: 275 VNMAATLLTGLVPLVIYLVSGKLFVRGIAAGAVKG 309 Lambda K H 0.330 0.146 0.461 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: 272 Number of extensions: 12 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: 268 Length of database: 309 Length adjustment: 26 Effective length of query: 242 Effective length of database: 283 Effective search space: 68486 Effective search space used: 68486 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: 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