Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF3640 PGA1_262p00440 xylose transport system permease protein XylH
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Phaeo:GFF3640 Length = 433 Score = 105 bits (263), Expect = 2e-27 Identities = 69/224 (30%), Positives = 119/224 (53%), Gaps = 22/224 (9%) Query: 116 AIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIA 175 A++A A ++GFV A++ +I A ++ G + G VG Sbjct: 229 AVIAGSIAASILGFV--AILNAYQIPAR----RLKRMMEAQGETMPEGLVVG-------- 274 Query: 176 LGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYI 235 +G+ + + + + +V ++ +T GR A GGNP+A+ L+GIN V I Sbjct: 275 ------YGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAELSGINTRLLTVKI 328 Query: 236 FLIQGAVTALAGVILASRITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVL 295 F + G + AL+ V+ ++R+ + + EL VI+A V+GG +L GG TI G ++G L Sbjct: 329 FALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSGGFGTIYGAILGAL 388 Query: 296 IMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQL--KNRGSR 337 IM ++++ M ++ +DA +Q +V G +L+AAV +D L K G+R Sbjct: 389 IMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKRVGAR 432 Score = 67.0 bits (162), Expect = 8e-16 Identities = 41/156 (26%), Positives = 73/156 (46%), Gaps = 13/156 (8%) Query: 38 LIVIFVVMFATMSLTVD-HFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTV 96 +I FV++ ++ D F + N+ L + + +++ M+F + +R DLSVG+ + Sbjct: 30 MIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDLSVGALL 89 Query: 97 AFAGVLCAMV------------LNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALI 144 A + A+V LN I + +A G +IG G ++ +L I A I Sbjct: 90 ATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFLTIPAFI 149 Query: 145 TTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLS 180 TL + R + + ++ GQ +G TF+ GG S Sbjct: 150 VTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVFGGTS 185 Lambda K H 0.326 0.139 0.396 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: 363 Number of extensions: 21 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: 338 Length of database: 433 Length adjustment: 30 Effective length of query: 308 Effective length of database: 403 Effective search space: 124124 Effective search space used: 124124 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 (21.7 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