Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 285 bits (730), Expect = 1e-81 Identities = 168/377 (44%), Positives = 233/377 (61%), Gaps = 28/377 (7%) Query: 1 MGQIQLTDLTKRFGDT--VAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSG 58 M ++L ++ K +G++ + D++L ID EFL+LVGPSGCGKST + +AGLE T G Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 DIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEV 118 +I + G+ ++ P++RDIAMVFQ YALYP M+VR NI FGL+ + +A+ +E V V Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRK-VPAAKIEEEVARV 119 Query: 119 AETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 178 A+ L I LL+RKP +LSGGQQQRVA+GRA+ R P+++L DEPLSNLDAKLR EMRTE++ Sbjct: 120 AKLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIK 179 Query: 179 NLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEP 238 + +L TTVYVTH+Q EAMT+ D++AVM DG +QQ +P E Y+ P NLFVA FIG P Sbjct: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSP 239 Query: 239 MINLV--RGTRSESTFVG----EHFSYPLDEDVMESVDDRD-DFVLGVRPEDIEVADAAP 291 +N V R + + +VG E S L + RD + +LG+RPE I +A A Sbjct: 240 PMNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGS 299 Query: 292 DDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPS----ADDALQAVTEGMHLVTRGDRV 347 D L +D+ VVEP G ++ + + A D V G+ + Sbjct: 300 -----ADFSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRV---------GETL 345 Query: 348 TVTIPPDKIHLFDAETG 364 + P + LFDA+TG Sbjct: 346 NLQFDPRRALLFDAQTG 362 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: 365 Number of extensions: 14 Number of successful extensions: 5 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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