Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >MicrobesOnline__882:209225 Length = 354 Score = 159 bits (402), Expect = 1e-43 Identities = 118/321 (36%), Positives = 166/321 (51%), Gaps = 34/321 (10%) Query: 16 EGGGDIVAVEEISLDID----DGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRV 71 EG G +A E+ D++ GE + LVGPSG GK+T LR +AGL+ EG +R+ Sbjct: 6 EGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRVTPPQ 65 Query: 72 LNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETT-----DM 126 +G + +VFQ Y L+PH SV N++FG + G+ +++RV D Sbjct: 66 GHGGG-----VVLVFQDYLLFPHLSVFENVAFG-PRARGVRGAALKERVHTMLRAFRLDT 119 Query: 127 LGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQ 186 ++ + R P QLS GQ+QRVAL RA+V DP V L+DEP +NLD LR EM ++ + Sbjct: 120 DDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVV 179 Query: 187 GELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMN 246 GV TV VTHD EA +GDR+ V+ G L Q+ PLD Y P + A F+G ++ Sbjct: 180 RRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLGPVTV- 238 Query: 247 LFDGSLSGDTFRGDGFDYPLSGAT--RDQLGGA---SGLTLGIRP----EDVTVGERRSG 297 L T R G D P + AT D + G L +RP V V R +G Sbjct: 239 -----LDETTRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRPWADGPAVLVSARFTG 293 Query: 298 QRTFDAEVVVVEPQGNENAVH 318 Q ++++ +G E VH Sbjct: 294 Q----VMQLLLDVEGQELLVH 310 Lambda K H 0.316 0.136 0.384 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: 373 Number of extensions: 22 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: 383 Length of database: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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 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