Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF3640 PGA1_262p00440 xylose transport system permease protein XylH
Query= uniprot:D8IUD2 (328 letters) >FitnessBrowser__Phaeo:GFF3640 Length = 433 Score = 117 bits (292), Expect = 7e-31 Identities = 89/291 (30%), Positives = 147/291 (50%), Gaps = 36/291 (12%) Query: 46 SAATFITLSNDIPPLVVMSVGMTFILIIGGIDLSVGS----VMALAASMLSMAMVRW--- 98 + A ++T I PL TF L+ GG ++G+ V+ + A++L++A + W Sbjct: 160 NVAWYLTDGQTIGPL-----DSTF-LVFGGTSGTLGTTLSWVVGIVATLLALAAL-WNSR 212 Query: 99 ------GWPLYAAAPLGVVVAALCGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQVTNS 152 G+P+ A V+ ++ ++ G V++ L +I ++ + Sbjct: 213 RAKQGHGFPVKPAWAEAVIAGSIAASILGFVAI----------LNAYQIPARRLKRMMEA 262 Query: 153 RTEYIGSAVDVISSPILFGMSPAFLSAIAIVIIAQLVLTRTVLGRYWIGIGTNEEAVRLS 212 + E + + V +G+ + L IA ++ ++ RT LGRY G N +A LS Sbjct: 263 QGETMPEGLVVG-----YGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAELS 317 Query: 213 GVNPNPSKILAFALMGALAGIAALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGR 272 G+N + FALMG L ++A+ +RL + G EL+VIAA VIGGT+L GG Sbjct: 318 GINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSGGF 377 Query: 273 GSIVSTFIGVLIISVLEAGLAQVGVSEPMKRIITGAVIVVAVILD-TYRRR 322 G+I +G LI+ L++G+A VGV P + I+ G V+V AV +D YR+R Sbjct: 378 GTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKR 428 Score = 63.9 bits (154), Expect = 7e-15 Identities = 55/236 (23%), Positives = 112/236 (47%), Gaps = 25/236 (10%) Query: 24 LGLMAALLAMCVMFAFLSEN-FLSAATFITLSNDIPPLVVMSVGMTFILIIGGIDLSVGS 82 LG++ A + +C+ F L++ FL+ L+ + +M+ GM F+++ IDLSVG+ Sbjct: 28 LGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDLSVGA 87 Query: 83 VMALAASMLSMAMV-----RWGWPLYAAA------PLGVVVAALCGTLTGMVSVHWRIPS 131 ++A ++++++ +G L A +G+ + L G G + IP+ Sbjct: 88 LLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFLTIPA 147 Query: 132 FIVSLGVLEIARGLAYQVTNSRTEYIGSAVDVISSPILFGMSPAFLSAIAIVIIAQLVLT 191 FIV+LG + R +A+ +T+ +T IG + S+ ++FG + L ++ +V T Sbjct: 148 FIVTLGGFLVWRNVAWYLTDGQT--IG---PLDSTFLVFGGTSGTLGTTLSWVVG-IVAT 201 Query: 192 RTVLGRYWIGIGTNEEAVRLSGVNPNPS---KILAFALMGALAGIAALFQVSRLEA 244 L W + A + G P+ ++A ++ ++ G A+ ++ A Sbjct: 202 LLALAALW----NSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPA 253 Lambda K H 0.325 0.137 0.392 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: 330 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 328 Length of database: 433 Length adjustment: 30 Effective length of query: 298 Effective length of database: 403 Effective search space: 120094 Effective search space used: 120094 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 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