Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 229 bits (585), Expect = 7e-65 Identities = 120/242 (49%), Positives = 164/242 (67%), Gaps = 3/242 (1%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 +Q T +++ FG+ AVD +S+DI D EF ++GPSG GK+T LR++AG E P+SG I I Sbjct: 5 VQFTQVSRTFGEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIRIQ 64 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 G P RD+ VFQDYAL+PHM V +NI +GL+ + G AER R E + Sbjct: 65 GVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVK-GVGKAERHSRAEEALAMVA 123 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 +A RKP +LSGGQ+QRVAL RA+V P V L+DEPL LD KLR +M+ EL+ LQ Q Sbjct: 124 LAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQ 183 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 L +T ++VTH+QTEA++M+DR+AV + G ++QV +P Y +P+ FVAEF+G N+V Sbjct: 184 LGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVGTS--NVV 241 Query: 244 RG 245 RG Sbjct: 242 RG 243 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: 285 Number of extensions: 12 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: 343 Length adjustment: 29 Effective length of query: 354 Effective length of database: 314 Effective search space: 111156 Effective search space used: 111156 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: 49 (23.5 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