Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 133 bits (335), Expect = 6e-36 Identities = 96/326 (29%), Positives = 160/326 (49%), Gaps = 18/326 (5%) Query: 8 RRF--EFQLFLVNVIIALFFYF------ENSAYFSSNNITTIFQYLAEIGIIAIGEAMLM 59 RRF E +FLV + I L F + S +S + + ++ IG++AIG ++ Sbjct: 18 RRFPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVI 77 Query: 60 LCGEIDLSPPALANFVPLITLTIYNS------IYQAISPTPAIVVSILLSLGLASLIGLM 113 + IDLS ++ +I ++ + ++ +++ P + + +++ LG+ L G + Sbjct: 78 ITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLP-VWIPVIVGLGVGLLAGAI 136 Query: 114 NGLITTKAKVNSLITTVGTLFLFNGIALIYSGGYPESFPYFRFLGGTVSILPVPFIWSLG 173 NG I + I T+G + G+A Y+ G P S + +PV I+ + Sbjct: 137 NGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPV-IIFLVV 195 Query: 174 ALVFLILLLHYTKIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSR 233 A++F I L YTK G +T A G N A G+ V R +I + I + L G++ +R Sbjct: 196 AVIFHIAL-RYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASAR 254 Query: 234 VLTIGATNFTADVVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAY 293 T G L+ IAAAVIGGTSL GG G + G +G++ + + +GF +G++AY Sbjct: 255 AAT-GQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAY 313 Query: 294 EFDAILGGAIVVVMVLSYYAKRASYK 319 D I G IVV +V+ Y + K Sbjct: 314 IQDIIKGLIIVVAVVIDQYRNKRKLK 339 Lambda K H 0.325 0.143 0.404 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: 307 Number of extensions: 25 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: 356 Length of database: 340 Length adjustment: 29 Effective length of query: 327 Effective length of database: 311 Effective search space: 101697 Effective search space used: 101697 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: 49 (23.5 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