Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate WP_079557323.1 CDL62_RS13615 substrate-binding domain-containing protein
Query= CharProtDB::CH_003787 (330 letters) >NCBI__GCF_002201795.1:WP_079557323.1 Length = 333 Score = 176 bits (446), Expect = 7e-49 Identities = 88/279 (31%), Positives = 164/279 (58%), Gaps = 2/279 (0%) Query: 54 LGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYD 113 LG V+SA N+ Q+ Q +++ GVD+L+I NG ++ +V++A++ G++V+AY+ Sbjct: 53 LGVNFIVRSAEDNDALQLRQGYELLDEGVDMLIIACVNGNTIAPLVRDAQRRGVRVIAYN 112 Query: 114 RMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLK 173 R+IN++D D +I+ +N+++ ++ A + + P GNY ++GG D N + +L Sbjct: 113 RLINNSDYDLFITGNNQQIAQIFCDAALRLKPSGNYVVLGGDRFDRNGLELKQHIDSILA 172 Query: 174 PYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQ 233 P+++SG+I ++ +V+ W A ++ L ++ IDAV+A +D GAI+ LS Sbjct: 173 PHIESGRINLIYSTFVENWSGTRARFELQQILESHGTDIDAVIACSDPMGVGAIELLSEY 232 Query: 234 GLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPK--ADT 291 GL G V ++GQDA L +++I G T+TVY P L + A++A E+ NG+ A+ Sbjct: 233 GLEGDVVVTGQDAILDAVRQIYNGNMTVTVYHPHRALGHRVADLAFEMLNGERSSRLANW 292 Query: 292 TLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330 NG ++P+ + + + + NI++ +I G + S++ Sbjct: 293 QTFNGFVEIPTYRMNSVAITRQNIEEELINVGQYTWSQI 331 Lambda K H 0.314 0.132 0.366 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: 229 Number of extensions: 11 Number of successful extensions: 2 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: 330 Length of database: 333 Length adjustment: 28 Effective length of query: 302 Effective length of database: 305 Effective search space: 92110 Effective search space used: 92110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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