Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_04155 Length = 369 Score = 281 bits (719), Expect = 2e-80 Identities = 164/367 (44%), Positives = 209/367 (56%), Gaps = 17/367 (4%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M + L ++ K + DT + D++LDI D EF+V VGPSGCGKST +RM+AGLE + GD+ Sbjct: 1 MASVTLRNIRKAYDDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 I G MN P R IAMVFQ YALYPHMT+ N+ FGL+ G E D V A+ Sbjct: 61 TINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLA-GTKKPEIDAAVRNAAK 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L I LLDRKP +LSGGQ+QRVA+GRAI R P+VFL DEPLSNLDA LR +MR E L Sbjct: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 D+L T +YVTH+Q EAMT+AD+I V+ G L+QV SP YH P N FVA FIG P + Sbjct: 180 HDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVD-----DRDDFVLGVRPEDIEVADAAPDDAA 295 N + G T G Y E +V+ D +G+RPE + V Sbjct: 240 NFMEGVVQSVTHDGVTVRYETGETQRVAVEPGAVKQGDKVTVGIRPEHLHV--------G 291 Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355 + D + VE GD L + + A D L A + +G+ + P+ Sbjct: 292 MTDDGVSARTMAVESLGDAAYL---YAESSVAPDGLIARIPPLERHAKGETQKLGATPEH 348 Query: 356 IHLFDAE 362 HLFD+E Sbjct: 349 CHLFDSE 355 Score = 25.0 bits (53), Expect = 0.004 Identities = 12/41 (29%), Positives = 20/41 (48%) Query: 341 VTRGDRVTVTIPPDKIHLFDAETGTAVHNRRHDQEADFTQL 381 V +GD+VTV I P+ +H+ + G + + D L Sbjct: 273 VKQGDKVTVGIRPEHLHVGMTDDGVSARTMAVESLGDAAYL 313 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: 384 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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