Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 290 bits (741), Expect = 6e-83 Identities = 174/377 (46%), Positives = 230/377 (61%), Gaps = 23/377 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +++ ++ K FG + D+SL ID EFL+LVGPSGCGKST + +AGLE TSG+I Sbjct: 1 MAALEINNVCKDFGSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGEI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 I G+ + ++ P RDIAMVFQ YALYP MTVRQNI FGLE + AER+ V VA+ Sbjct: 61 RIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRK-VPKAEREAAVERVAD 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L I LL+RKP +LSGGQ+QRVA+GRA+ R+P+V+L DEPLSNLDAKLR +MRTE++ L Sbjct: 120 LLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L T VYVTH+Q EAMT+AD IAVM DG + Q+ SP E Y++P +LFVA F+G P + Sbjct: 180 HQRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSM 239 Query: 241 NLVRGT--------RSESTFVGE---HFSYPLDED---VMESVDDRDDFVLGVRPEDIEV 286 N + T R GE +P + + + E V +R +LG+RPE Sbjct: 240 NFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGER--VILGLRPEHFTE 297 Query: 287 ADAAPDDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDR 346 DA + A + L +TVVEP G +L L D A V G+R Sbjct: 298 DDARLGEYA-EGVALTPRITVVEPTGADILLQLK-----LGDGEATARVGPKCRVKAGER 351 Query: 347 VTVTIPPDKIHLFDAET 363 +T+ I + +FD ET Sbjct: 352 LTLRIDMGRAVMFDRET 368 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: 354 Number of extensions: 17 Number of successful extensions: 3 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: 373 Length adjustment: 30 Effective length of query: 353 Effective length of database: 343 Effective search space: 121079 Effective search space used: 121079 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 24 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