Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate H281DRAFT_03877 H281DRAFT_03877 xylose-binding protein
Query= CharProtDB::CH_003787 (330 letters) >FitnessBrowser__Burk376:H281DRAFT_03877 Length = 342 Score = 383 bits (983), Expect = e-111 Identities = 193/320 (60%), Positives = 248/320 (77%), Gaps = 3/320 (0%) Query: 13 SLLLTNVAAHAKE--VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQ 70 SL L AHA + +IG IDDLR+ERW +DRD FV AE LGAKV VQSA+ +E Q Sbjct: 21 SLSLAAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQSADASEARQ 80 Query: 71 MSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNE 130 +SQIEN+I+RGVDV+VI+P+N + L NVV EA++ GIKV++YDR+I DAD+D YISFDNE Sbjct: 81 ISQIENLISRGVDVIVIVPFNSKTLGNVVAEARKAGIKVVSYDRLILDADVDAYISFDNE 140 Query: 131 KVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVD 190 KVGELQA+ + P+GNYFL+GG+P DNNAK+ R GQ+KVLKP +D G IK+VG QWV Sbjct: 141 KVGELQAEGVYKAQPKGNYFLLGGAPTDNNAKMLREGQLKVLKPAIDKGDIKLVGQQWVP 200 Query: 191 GWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAG 250 W AL+I+E+ALTANNNKIDA+VASND TAGGAIQAL+AQ ++GKV +SGQDADLA Sbjct: 201 EWSASTALRIVEDALTANNNKIDAIVASNDGTAGGAIQALAAQHMAGKVPVSGQDADLAA 260 Query: 251 IKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDV 310 +KR+ AGTQTMTVYKP+ L+A AA+++V L G++P + +NG K V + LL P + Sbjct: 261 VKRLIAGTQTMTVYKPLKLIAGEAAKLSVALAKGEKPAFNAQYDNGKKKVDTVLLQPTLL 320 Query: 311 NKNNIKDTVIKDGFHKESEL 330 K+N+ D VIKDGF+ +++L Sbjct: 321 TKSNV-DVVIKDGFYTQAQL 339 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: 359 Number of extensions: 14 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: 342 Length adjustment: 28 Effective length of query: 302 Effective length of database: 314 Effective search space: 94828 Effective search space used: 94828 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 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