Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate Echvi_1284 Echvi_1284 ABC-type sugar transport system, periplasmic component
Query= CharProtDB::CH_003787 (330 letters) >FitnessBrowser__Cola:Echvi_1284 Length = 316 Score = 87.8 bits (216), Expect = 3e-22 Identities = 82/287 (28%), Positives = 130/287 (45%), Gaps = 10/287 (3%) Query: 4 KNILLTLCTSLLLTNV----AAHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVF 59 +NIL+ LLL +A + K+ + + L + + K+AESLG +V Sbjct: 6 QNILIWCLPLLLLVGACESNSATETKGKVAVIVSTLNNPWFVVLAETAAKEAESLGYEVS 65 Query: 60 VQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDA 119 + + N + + EN I G ++ P + + + V +A + GI V DR +N + Sbjct: 66 IFDSQNNTALENNHFENAITAGYQAILFNPTDAEGSVSNVTKASEAGIAVFCMDREVNSS 125 Query: 120 DIDFYISFDNEKVGELQAKALVDIVPQ-GNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDS 178 I DN K VD + + GNY + G DNN G V+ Y D Sbjct: 126 LPTSQILSDNYAGCVSLGKYFVDQLDKSGNYVEILGLVGDNNTWNRSKGFHSVVGHYPD- 184 Query: 179 GKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGK 238 +K+V Q D + A+++ME+ L + + IDAV NDA A GA QAL A GL + Sbjct: 185 --LKMVAQQSAD-FDRNKAMEVMESILQVHRD-IDAVFCGNDAMAMGAYQALKAAGLENQ 240 Query: 239 VAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQ 285 V + G D + + G T + ++A TAA++A + G+ Sbjct: 241 VMVFGFDGAADVVDAVKDGRIAATAMQFPKVMAKTAAQLADKYIQGE 287 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: 223 Number of extensions: 16 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: 316 Length adjustment: 28 Effective length of query: 302 Effective length of database: 288 Effective search space: 86976 Effective search space used: 86976 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: 48 (23.1 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