Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 (characterized)
to candidate GFF2207 HP15_2161 sugar ABC transporter, permease protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3040 (276 letters) >FitnessBrowser__Marino:GFF2207 Length = 269 Score = 142 bits (359), Expect = 6e-39 Identities = 74/253 (29%), Positives = 130/253 (51%) Query: 23 ILIFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHINERSDYFSFAWNSVVISFSA 82 +L+ PI+W++ SFKT + + TL+NY I +++ NS++ Sbjct: 17 LLLLTPIYWLLNMSFKTNQEILGGLTLWPQNFTLDNYAVIFTDPSWYNGYINSMIYVSIN 76 Query: 83 TALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIA 142 + LL+A+PAAY+ + Y+ + W+LS +M PP L+P + L S GL DT IA Sbjct: 77 VVITLLVALPAAYAFSRYKFLGDKHLFFWLLSNRMAPPAVFLLPFFQLYSSIGLFDTHIA 136 Query: 143 LIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQEMLRVLLPIAKGGLASTVL 202 + + + L N+P+ VW++ + +PR+ E A +DG + + ++V LP+ + G+ T Sbjct: 137 VALAHCLFNVPLAVWILEGFMSGVPREYDEMAYIDGYSFPKFFVKVFLPMIRSGIGVTAF 196 Query: 203 LSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWIS 262 + + W E + LTS A P+ A++ G+ W L+A +L P L+ W Sbjct: 197 FAFMFSWVELLLARTLTSVDAQPIGAIMTRTIGASGIDWGVLAAAGSLTIIPGLLVIWFV 256 Query: 263 QKQLVRGLSFGAV 275 + + +G + G V Sbjct: 257 RNHVAKGFALGRV 269 Lambda K H 0.328 0.138 0.427 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: 243 Number of extensions: 17 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: 269 Length adjustment: 25 Effective length of query: 251 Effective length of database: 244 Effective search space: 61244 Effective search space used: 61244 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