Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 293 bits (751), Expect = 4e-84 Identities = 166/361 (45%), Positives = 229/361 (63%), Gaps = 15/361 (4%) Query: 8 DVTKVYTDEGGGD--IVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGEL 65 D+ + G GD + + ++ + + GEFL+LVGPSGCGKST L ++AGL+ TEGE+ Sbjct: 6 DIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEI 65 Query: 66 RLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTD 125 R+ + + G+ +DRDIAMVFQSYALYP SV N+ F LE +P E ++R++E Sbjct: 66 RIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRK-MPKPERQKRIDEVAA 124 Query: 126 MLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRL 185 ML IS LLDR+P QLSGGQ+QRVA+GRA+ R P++FL DEPLSNLDAKLR EMR E++RL Sbjct: 125 MLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRL 184 Query: 186 QGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSM 245 G+T+VYVTHDQ EAMT+G R+AV+ G +QQ+GTP + Y+RP N +VA FIG P+M Sbjct: 185 HQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTM 244 Query: 246 NLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEV 305 NL G+++G F G L+ A+ + LG+RPE + + E + V Sbjct: 245 NLLRGAVTGGQFGIQGAALNLAPPP----SSANEVLLGVRPEHLVMQE----TAPWRGRV 296 Query: 306 VVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGETGDA 365 VVEP G + V VD G+ T T Q+RV+ G+ ++ H FD ++ + Sbjct: 297 SVVEPTGPDTYV---MVDTAAGS-VTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEER 352 Query: 366 L 366 L Sbjct: 353 L 353 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: 18 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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