Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_03749 Length = 360 Score = 298 bits (762), Expect = 2e-85 Identities = 174/371 (46%), Positives = 220/371 (59%), Gaps = 22/371 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +QL+ + KR+GDT V + L IDD EF+VLVGPSGCGKST +RM+AGLE + GD+ Sbjct: 1 MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 IGG N PQ R+I+MVFQ YALYPH++V +NI FG + + A R+ A+ Sbjct: 61 MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKE-SPANFKPRIEAAAK 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L + LDR P LSGGQ+QRVA+GRA+VR+P +FL DEPLSNLDAKLR +MRTE++ L Sbjct: 120 MLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKAL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L T +YVTH+Q EAMTMADRI VM+ G ++Q+ P E Y P NLFVA F+G P + Sbjct: 180 HQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSM 239 Query: 241 NLVRGTRSESTFVGEHFSYPL---DEDVME----SVDDRDDFVLGVRPEDIEVADAAPDD 293 N G T G + L E V+E S LGVRPE IE P Sbjct: 240 NFAEGVLVNRT-QGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTP-- 296 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353 D+ M V VVEP G + +H D T V G+RVT+ +P Sbjct: 297 ------DVTMQVEVVEPTGAE-----THLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPA 345 Query: 354 DKIHLFDAETG 364 IHLFD E+G Sbjct: 346 AHIHLFDTESG 356 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: 378 Number of extensions: 22 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: 360 Length adjustment: 30 Effective length of query: 353 Effective length of database: 330 Effective search space: 116490 Effective search space used: 116490 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