Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 214 bits (544), Expect = 4e-60 Identities = 129/357 (36%), Positives = 196/357 (54%), Gaps = 12/357 (3%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G A+ ++LDI +GE + L+GPSG GK+T LR++AGLE G + +R + V + Sbjct: 13 GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFGNRDVTQVHVR 72 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLE---ESTGLPDDEIRQRVEETTDMLGISDLLDR 135 DR + VFQ+YAL+ H +V N++FGLE + EI++RV +M+ + L R Sbjct: 73 DRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLLEMVQLGHLAQR 132 Query: 136 KPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVY 195 P QLSGGQ+QR+AL RA+ PEV L+DEP LDAK+R E+R L+ L EL T+V+ Sbjct: 133 YPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVF 192 Query: 196 VTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255 VTHDQ EA+ + DRV V+ +G ++QV TP++ Y +PN+ FV F+G ++N F+ + + Sbjct: 193 VTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG--NVNRFEANWQQN 250 Query: 256 TF-RGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNE 314 + GD F P Q G L +R ++ + ++ + Q +V + P G E Sbjct: 251 RWTNGDAFIVPPEQTPLQQNG-----ALYVRSHELALADKPNSQAHIPFTIVAITPIGAE 305 Query: 315 NAVHLRFVDGDEGTQFTATTTGQSRVEAG-DRTTVSFPEDAIHLFDGETGDALKNRE 370 V L + + A T E G + +V + F G+ GD R+ Sbjct: 306 VRVELAPIGWQSEELWEAKFTHHHLQELGLQKGSVVYATPRTGYFFGKQGDGSPIRQ 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: 379 Number of extensions: 21 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: 376 Length adjustment: 30 Effective length of query: 353 Effective length of database: 346 Effective search space: 122138 Effective search space used: 122138 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