Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 204 bits (519), Expect = 3e-57 Identities = 113/297 (38%), Positives = 178/297 (59%), Gaps = 16/297 (5%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G+ VA++++SL I GE + L+GPSGCGK+T LR++AG+ET EG++ E + A+ Sbjct: 13 GNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHAR 72 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLP---DDEIRQRVEETTDMLGISDLLDR 135 +R + VFQ YAL+ H +V N++FGL + EIR+RV + ++ + L DR Sbjct: 73 ERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADR 132 Query: 136 KPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVY 195 P QLSGGQ+QR+AL RA+ +P+V L+DEP LD K+R E+R L+RL E+ +++V+ Sbjct: 133 YPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVF 192 Query: 196 VTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255 VTHDQ EA+ + DRV V++ G ++QVG+P + Y P + FV F+G ++N+F + G Sbjct: 193 VTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLG--NVNVFHSRVHG- 249 Query: 256 TFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQG 312 + RD + IRP D+ + + + + +A+V V+ G Sbjct: 250 ---------AWAEVARDDVPAGQEAVAFIRPHDIDI-DTVATPESLEAKVSYVQTIG 296 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: 348 Number of extensions: 15 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: 360 Length adjustment: 30 Effective length of query: 353 Effective length of database: 330 Effective search space: 116490 Effective search space used: 116490 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 Apr 09 2024. 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