Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 290 bits (743), Expect = 3e-83 Identities = 171/380 (45%), Positives = 234/380 (61%), Gaps = 30/380 (7%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L +++V K + E ++++SL ID GEFL+LVGPSGCGKST + +AGLE V Sbjct: 1 MAALEINNVCKDFGSEQ-----VLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T GE+R+ + + +RDIAMVFQSYALYP +VR N+SFGLE +P E V Sbjct: 56 TSGEIRIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRK-VPKAEREAAV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E D+L I LL+RKP QLSGGQ+QRVA+GRA+ R+P+V+L DEPLSNLDAKLR +MRT Sbjct: 115 ERVADLLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRT 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+++L LG T VYVTHDQ EAMT+ D +AV+ DG + Q+G+P + Y+ P +LFVAGF+ Sbjct: 175 EIKKLHQRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFM 234 Query: 241 GEPSMNLFDGSLSG---------DTFRGDGFDYPL-----SGATRDQLGGASGLTLGIRP 286 G PSMN +L G +T + + P + A +++G + LG+RP Sbjct: 235 GSPSMNFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVG--ERVILGLRP 292 Query: 287 EDVTVGERRSGQR----TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEA 342 E T + R G+ + VVEP G + + L+ DG+ TA + RV+A Sbjct: 293 EHFTEDDARLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEA----TARVGPKCRVKA 348 Query: 343 GDRTTVSFPEDAIHLFDGET 362 G+R T+ +FD ET Sbjct: 349 GERLTLRIDMGRAVMFDRET 368 Lambda K H 0.316 0.136 0.384 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: 439 Number of extensions: 29 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: 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: 42 (22.0 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