Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein
Query= uniprot:Q4J711 (356 letters) >NCBI__GCF_002095475.1:WP_084931761.1 Length = 323 Score = 147 bits (370), Expect = 5e-40 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 20/304 (6%) Query: 19 VIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLS--PPALANFVP 76 +II + F F + +F+ N+ I Q + +IA+G ++++ G IDLS P A + V Sbjct: 31 LIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAALSAVL 90 Query: 77 LITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTVGTLFLF 136 TL + A P P V+IL +LG+ +L G+ +G++ A + I T+G L LF Sbjct: 91 GATLMV------AGVPVP---VAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLF 141 Query: 137 NGIALIYSGGYPE---SFPYFRFLGGTVSILPVPFIWSLGALVFLILLLHYTKIGVWTIA 193 IALIY+GG P + + V +P P I + L L+++ T +G + +A Sbjct: 142 RAIALIYTGGNPVFGIPMEFRSIINSDVFGIPTPIIIVAVIALVLWLVMNKTPLGEYILA 201 Query: 194 AGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTADVV--LEGI 251 G N A GVPV R K+ FII + +L +I R +GA T + L+ I Sbjct: 202 VGGNEEAARVAGVPVKRTKVTVFIISGTLASLASLILIGR---LGAAEPTIGNLWELDAI 258 Query: 252 AAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVVVMVLSY 311 AAA IGG SL+GGKGS+VG +G++ + L NG +L I A+ + + G I+++ +L Sbjct: 259 AAAAIGGASLMGGKGSIVGTIIGAIILGALRNGLTLLNIQAF-YQLLATGLIIIIAMLID 317 Query: 312 YAKR 315 A R Sbjct: 318 RATR 321 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: 354 Number of extensions: 33 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: 323 Length adjustment: 28 Effective length of query: 328 Effective length of database: 295 Effective search space: 96760 Effective search space used: 96760 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 24 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