Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 229 bits (585), Expect = 7e-65 Identities = 132/280 (47%), Positives = 179/280 (63%), Gaps = 17/280 (6%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G+ + V +++LDI GEFL L+GPSG GK+T+L M+AG ET T GE+ L+ R +N V Sbjct: 22 GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRAINNVPPH 81 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138 RD+ MVFQ+YAL+PH +V N++F L G+ +I++RV+ M+ + +R P Sbjct: 82 KRDMGMVFQNYALFPHMTVSENLAFPLSVR-GMAKPDIKERVKRALAMVQLEGFRNRYPA 140 Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198 QLSGGQQQRVAL RA+V +P++ LMDEPL LD +LR +M+ E++ L LGVT VYVTH Sbjct: 141 QLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVTVVYVTH 200 Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPS---MNLFDGSLSGD 255 DQ EA+TM DRVAV G++QQ+ P Y +P N FVA F+GE + +L D Sbjct: 201 DQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLPAHLLDR----- 255 Query: 256 TFRGDGFDYPLS-GATRDQLG---GASG--LTLGIRPEDV 289 RGD L G T + L GA+G ++L IRPE V Sbjct: 256 --RGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPERV 293 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: 420 Number of extensions: 17 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: 369 Length adjustment: 30 Effective length of query: 353 Effective length of database: 339 Effective search space: 119667 Effective search space used: 119667 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