Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate AO356_28585 AO356_28585 ABC transporter
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 280 bits (716), Expect = 5e-80 Identities = 162/373 (43%), Positives = 229/373 (61%), Gaps = 17/373 (4%) Query: 3 RLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTE 62 +L LD+V K GG I+ ++SL+I GEF+V VGPSGCGKST LR++AGL+++ Sbjct: 3 KLKLDNVNKQL---GGARIL--RDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICG 57 Query: 63 GELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEE 122 G+L ++ R +N + ++R + MVFQSYALYPH SV N+SFGL+ + +R+RV + Sbjct: 58 GDLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAK-TEKTSLRERVLK 116 Query: 123 TTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTEL 182 T +L + LL RKP +LSGGQ+QRVA+GRA+ R+P++ L DEPLSNLDA LR +MR E+ Sbjct: 117 TAQILQLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEI 176 Query: 183 QRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGE 242 RL G LG T +YVTHDQ EAMT+ D++ VL+ G ++QVG+P + Y RP + FVAGF+G Sbjct: 177 ARLHGRLGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGS 236 Query: 243 PSMNLFDGSL--SGDTFRGDGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGERRSGQ 298 P MN L G+T + + ++ D G A+ L+LGIRPE + + ++ Q Sbjct: 237 PRMNFLAAFLHTPGETSQVESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIAL---KAAQ 293 Query: 299 RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLF 358 T V VE G+E VHL D + + GDR + D +H+F Sbjct: 294 GTAGIAVSGVEYLGSETYVHL---DTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVF 350 Query: 359 DGETGDALKNREL 371 D G AL+ + Sbjct: 351 DTH-GTALQRHAI 362 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: 404 Number of extensions: 22 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: 383 Length of database: 379 Length adjustment: 30 Effective length of query: 353 Effective length of database: 349 Effective search space: 123197 Effective search space used: 123197 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: 50 (23.9 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