Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 291 bits (744), Expect = 3e-83 Identities = 172/377 (45%), Positives = 229/377 (60%), Gaps = 20/377 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M I++ +L K FG + + L+I D EF+ +GPSGCGKST LR +AGLE G I Sbjct: 1 MATIRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 +G + RDIAMVFQ+YALYPHM VR+N+ FGL G E D RV AE Sbjct: 61 RLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALN-GMKRNEIDRRVNNAAE 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L I +LLDRKP +LSGGQ+QRVA+GRAIVR+P++FL+DEPLSNLDA LR MR EL L Sbjct: 120 ILRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAAL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 ++L VT +YVTH+Q EAMT++DR+ V+D G + Q +P E ++ P NLFVA FIG P + Sbjct: 180 HERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRM 239 Query: 241 NLVRGTRSES-----TFVGEHFSYP--LDEDVMESVDDRDDFVLGVRPEDIEVADAAPDD 293 N + +E T G S P LD ES++ LG+RP+ +E+ +P++ Sbjct: 240 NFLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLEL--TSPEE 297 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353 A L V +VE G ++ +H+ + L AV G H V D+V + +PP Sbjct: 298 A-----HLAGTVRLVERLGTESHVHI----RVEGGGDLTAVVRGTHPVASRDQVHLRLPP 348 Query: 354 DKIHLFDAETGTAVHNR 370 + HLFDAE GTA+ R Sbjct: 349 EHCHLFDAE-GTAIARR 364 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: 416 Number of extensions: 21 Number of successful extensions: 4 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: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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 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