Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate SMa0070 SMa0070 ABC transporter permease
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__Smeli:SMa0070 Length = 327 Score = 149 bits (376), Expect = 1e-40 Identities = 94/316 (29%), Positives = 161/316 (50%), Gaps = 18/316 (5%) Query: 14 LFLVNVIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPPALAN 73 L L+ V++ +F N S N+ + L E+ ++AIG +LM+CGE DLS ++ Sbjct: 17 LALLFVLVLVFQAKSNGILLSFENMRGVMGLLPEMALVAIGVTLLMICGEFDLSVGSVFA 76 Query: 74 FVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTVGTL 133 +P+ + NS V++LL L + IG +NG +T + + S ITT+G L Sbjct: 77 LMPMSMAVLLNS-------GVPFTVAVLLGLMICGAIGFINGYVTLQFSIPSFITTLGML 129 Query: 134 FLFNGIALIYSGGYPESFP------YFRFLGGTVSILPVPFIWSLGALVFLILLLHYTKI 187 F+ + ++ SGG+P P F S + F+W + + LL T Sbjct: 130 FIARSLTIVISGGFPPLLPPDLPTWLFTDYIWQGSPFRMSFLWFVVIAALVAALLSLTNF 189 Query: 188 GVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGAT--NFTAD 245 G W A G A+ +G+PV RVKI+ F++ + + G++Q VL +G+ + Sbjct: 190 GNWIRATGGFNEAAASMGIPVKRVKIVCFMLCSVLAGFAGLLQ---VLRLGSPLPSIGEG 246 Query: 246 VVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVV 305 + L+ +AAAVIGGT+L GG G++ GA +G++ I + NG + ++A F +G + Sbjct: 247 LELQAVAAAVIGGTALAGGIGTVFGAIIGTLLIRTIDNGLVLSRVDANWFKFAIGVLTMF 306 Query: 306 VMVLSYYAKRASYKLK 321 ++ + + + S K+K Sbjct: 307 AVIANAWMGKMSRKIK 322 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: 306 Number of extensions: 15 Number of successful extensions: 4 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: 327 Length adjustment: 29 Effective length of query: 327 Effective length of database: 298 Effective search space: 97446 Effective search space used: 97446 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