Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544740.1 B9Y55_RS07445 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_900177735.1:WP_085544740.1 Length = 497 Score = 159 bits (403), Expect = 8e-44 Identities = 84/235 (35%), Positives = 146/235 (62%), Gaps = 2/235 (0%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 +E+R++ K FG V ALD V + ++ GE+ L G NG+GKSTLIKIISG ++P+ G +F Sbjct: 8 IELRNISKRFGGVTALDDVGLSLSPGEIHCLAGQNGSGKSTLIKIISGVYRPEDGAEIFI 67 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREV-TNKIFLNKKKMMEESKK 123 +++ P A +GI+ IYQDL++ P L + NI L + + F++K +++ ++K Sbjct: 68 DGELVALDPAKAIGIGIQVIYQDLSIFPGLSVAENIGLGQYCEKGRFFVDKGRLVSDAKT 127 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 ++ + I +P + KV LS RQ VA+ RA+ A++++MDEPTA+L+ E + +L + Sbjct: 128 AMNKIGISLP-LRKKVSELSIADRQLVAICRALANDARLVIMDEPTASLTRTEVKALLSV 186 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 + LK + + V+ ++H + + EVA+R+ VL GK + + E + +++ MT Sbjct: 187 VKELKNRDIAVVFVSHRLDEVIEVAERVTVLRDGKSVGVFEASELDDKKLATYMT 241 Score = 99.8 bits (247), Expect = 1e-25 Identities = 58/219 (26%), Positives = 114/219 (52%), Gaps = 10/219 (4%) Query: 23 VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82 VS E+++GE++ + G G+G++ L + G + PD G + EGK + +S D GI Sbjct: 274 VSFELHRGEILGITGLLGSGRTELALSLFGKNPPDSGTIALEGKYLSLSSIRDGIYSGIG 333 Query: 83 TIYQD---LALIPDLPIYYNIFLA-----REVTNKIFLNKKKMMEESKKLLDSLQIRIPD 134 + +D L ++ D I N L + I K+ + S + L +++ D Sbjct: 334 YVSEDRLTLGIVMDQSIRDNSVLTVLDRLKSSFGTIDGTKRDQLVSSS--VQELSVKVSD 391 Query: 135 INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGV 194 +N+ V LSGG +Q V +A+ + K++++D PT + + + + ++ ++L KG+G+ Sbjct: 392 VNLPVRTLSGGNQQKVVLAKWLATKPKVLILDSPTVGVDIAAKKGIYDIVKSLSAKGMGI 451 Query: 195 LIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233 ++I+ I + Y RI + RG+I + ET+ +++ Sbjct: 452 IMISDEIPEVYYNCHRIITMQRGRITGEYRPTETSEQDL 490 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: 297 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 251 Length of database: 497 Length adjustment: 29 Effective length of query: 222 Effective length of database: 468 Effective search space: 103896 Effective search space used: 103896 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: 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