Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 209 bits (532), Expect = 1e-58 Identities = 115/284 (40%), Positives = 173/284 (60%), Gaps = 11/284 (3%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 +++ + K F + A+ D+ L + E L +GPSGCGK+T LR++AGLET TSG I Sbjct: 20 LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 G +++ RD +VFQ YAL+P++T+ +N+ +GL + AE RV E+ G Sbjct: 80 GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGK-MRKAEIQARVAELLAMAG 138 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 + + P +LSGGQQQRVAL RA+ +P + L+DEPLS LDA +R +R E++ LQ Q Sbjct: 139 LPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQ 198 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 + +TT+ VTH+Q EA++M+DRI VM+ G ++QV +P E Y P + FVA F+G+ +N++ Sbjct: 199 VGITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVL 256 Query: 244 RGTRSESTFVGEHFSYPLDEDVMESVDDR----DDFVLGVRPED 283 RG G+ F E E+ + +D L +RPED Sbjct: 257 RG----QALGGKRFRVGKMEIECEASEGSFRLGEDVSLYLRPED 296 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: 310 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: 377 Length adjustment: 30 Effective length of query: 353 Effective length of database: 347 Effective search space: 122491 Effective search space used: 122491 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