Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate WP_085126662.1 B9O00_RS29725 D-xylose ABC transporter substrate-binding protein
Query= CharProtDB::CH_003787 (330 letters) >NCBI__GCF_900177295.1:WP_085126662.1 Length = 345 Score = 246 bits (628), Expect = 6e-70 Identities = 136/321 (42%), Positives = 194/321 (60%), Gaps = 9/321 (2%) Query: 15 LLTNVAAHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQI 74 L + +A A + +G++ + + ERW+ D E GA+ A + Q+S + Sbjct: 16 LSSTLALAADPLIVGVSWSNFQEERWKTDEAAIKAALEKAGARYISTDAQSSSAKQLSDV 75 Query: 75 ENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGE 134 E++I+RG + L+I+ + + + A EGI V+ YDR+I D FY++FDN++VG Sbjct: 76 ESLISRGANALIILAQDAAAIGPAINAADAEGIPVVGYDRLIEDPRA-FYLTFDNKEVGR 134 Query: 135 LQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLP 194 +QA+A+ D P+GNY + GSP D NA +GQM+VLKP +D G IKVVG Q+ DGWLP Sbjct: 135 MQAQAVYDKQPKGNYVFILGSPTDPNADFLFSGQMEVLKPAIDKGDIKVVGKQYTDGWLP 194 Query: 195 ENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRI 254 NA + ME LTA NNK+DAVVASND TAGG + AL+AQG+ G + +SGQD D A + R+ Sbjct: 195 ANAQRNMEQILTATNNKVDAVVASNDGTAGGVVAALTAQGMQG-IPVSGQDGDHAALNRV 253 Query: 255 AAGTQTMTVYKPITLLANTAAEIAVELGNGQ-----EPKADTTLNNGLKDVPSRLLTPID 309 A GTQT++V+K L AAEIAV L G+ E T NG K + S+ L P+ Sbjct: 254 ALGTQTVSVWKDARALGKRAAEIAVALAKGKKLSEIEGAESWTSPNG-KTLSSQFLKPVP 312 Query: 310 VNKNNIKDTVIKDGFHKESEL 330 + + N+ D VI G+ E+ Sbjct: 313 ITRKNL-DVVIDAGWITRQEV 332 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: 279 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: 345 Length adjustment: 28 Effective length of query: 302 Effective length of database: 317 Effective search space: 95734 Effective search space used: 95734 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 Apr 09 2024. 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