Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate WP_032993719.1 RL_RS29730 sugar ABC transporter substrate-binding protein
Query= CharProtDB::CH_003787 (330 letters) >NCBI__GCF_000009265.1:WP_032993719.1 Length = 354 Score = 149 bits (376), Expect = 1e-40 Identities = 99/299 (33%), Positives = 154/299 (51%), Gaps = 17/299 (5%) Query: 41 QKDRDIFVKKAESLGA--KVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNV 98 + D FV + + L A KV Q+A+ + Q Q + I +G V+V+ P + +++ Sbjct: 48 EHDHPGFVAEMKKLCASCKVLYQNADADIAKQQQQFNSAITQGAKVIVLDPVDSAAAASL 107 Query: 99 VKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQ-------GNYFL 151 V+ A+ +G+KV+AYDR I DFY+SFDN+ +G+ A++LV + G Sbjct: 108 VQLAQSQGVKVIAYDRPIPKGKADFYVSFDNKAIGKAIAESLVQHLKAQKVPTDGGGILQ 167 Query: 152 MGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNK 211 + GSP D A L + G + L SG+ K + + W P NA + +T + Sbjct: 168 INGSPTDAAAGLIKDGIHEGLA----SGEYKTLAEFDTPNWQPANAQQWAGGQITRFGKQ 223 Query: 212 IDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLA 271 I VVA+ND T GGAI A A G+ ++G DA +A ++ I +G Q T+ KP ++A Sbjct: 224 IVGVVAANDGTGGGAIAAFKAAGVDPVPPVTGNDATIAALQLIISGDQYNTISKPSEIVA 283 Query: 272 NTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330 AA +AV+L G+ KA+ T L D P++L P V N+K +I + EL Sbjct: 284 AAAANVAVKLLAGETIKAEMT----LYDTPAQLFVPAVVTAENLKAEIIDKKINTAEEL 338 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: 275 Number of extensions: 10 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: 330 Length of database: 354 Length adjustment: 29 Effective length of query: 301 Effective length of database: 325 Effective search space: 97825 Effective search space used: 97825 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