Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 226 bits (576), Expect = 8e-64 Identities = 117/249 (46%), Positives = 170/249 (68%), Gaps = 8/249 (3%) Query: 4 LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63 LTL +++K + + + + +L I DGEF ++GPSGCGK+T LR++AG E EG Sbjct: 7 LTLSNISKRFASQE-----VLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEG 61 Query: 64 ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123 ++ L + + A+ R VFQSYAL+PH +V N++FGL+ + G+ +I RV + Sbjct: 62 QILLNGDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMA-GVDVQDIAVRVADA 120 Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183 ++ +S+ RKP QLSGGQ+QRVA+ RA+V P++ L+DE LS LD KLR +M+ EL+ Sbjct: 121 LAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELK 180 Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243 +LQ +LG+T VYVTHDQ EA++M DR+ V+ +G+ QQVGTP + Y P NLFVA FIGE Sbjct: 181 QLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE- 239 Query: 244 SMNLFDGSL 252 +N+FDG + Sbjct: 240 -INVFDGEI 247 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: 399 Number of extensions: 19 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 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