Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Cola:Echvi_1333 Length = 243 Score = 116 bits (291), Expect = 4e-31 Identities = 74/230 (32%), Positives = 124/230 (53%), Gaps = 6/230 (2%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L ++ K + K ++ +S+E+ +GE+V LLG NGAGK+T +I G KP+ G VF Sbjct: 2 ILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGK-VF 60 Query: 64 EGKKVIFNSPNDARS-LGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESK 122 K+ I P R+ LGI + Q+ ++ L + NI E+TN L K E+ + Sbjct: 61 LDKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIMAVLEMTN---LPKAAQKEKME 117 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +LL+ + N+ + LSGG+R+ +ARA+ K +L+DEP A + + ++ Sbjct: 118 ELLEEFSLTHVRKNLGMV-LSGGERRRTEIARALAVDPKFVLLDEPFAGVDPIAVEEIQT 176 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEE 232 + LK K +G+LI HN+ + + DR Y++ GK++ EE +E Sbjct: 177 IVAKLKNKNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAADE 226 Lambda K H 0.318 0.137 0.371 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: 170 Number of extensions: 11 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: 251 Length of database: 243 Length adjustment: 24 Effective length of query: 227 Effective length of database: 219 Effective search space: 49713 Effective search space used: 49713 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: 41 (21.7 bits) S2: 46 (22.3 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