Align Xylose/arabinose import ATP-binding protein XacJ; 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:D4GP38 (383 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 227 bits (579), Expect = 4e-64 Identities = 130/300 (43%), Positives = 183/300 (61%), Gaps = 18/300 (6%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 + L++++KRF + D +L I D EF ++GPSGCGK+T LR++AG E P G I + Sbjct: 7 LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 GD + + R VFQ YAL+PH+TV N+ FGL+ + + V VA+ L Sbjct: 67 GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLK----MAGVDVQDIAVRVADALA 122 Query: 124 IADLLD---RKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 I L + RKP +LSGGQ+QRVA+ RA+V P++ L+DE LS LD KLR +M+ EL+ L Sbjct: 123 IVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQL 182 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 Q QL +T VYVTH+Q EA++M+DRI VM +G+ QQV +P E Y P NLFVA+FIGE I Sbjct: 183 QRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--I 240 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLG------VRPEDIEVADAAPDDA 294 N+ G ++ +GE+ V+ + F +G +RPED+ + D PD A Sbjct: 241 NVFDGEIVQA--LGEYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRI-DCRPDVA 297 Lambda K H 0.317 0.135 0.386 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: 9 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: 41 (21.6 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