Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 296 bits (757), Expect = 8e-85 Identities = 172/375 (45%), Positives = 230/375 (61%), Gaps = 23/375 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M++L L + K Y G ++ I +DI GEFL+LVGPSGCGKST + +AGLET+ Sbjct: 1 MSQLELRSIRKTYP---GVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETI 57 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T+G + L+ + ++ + +DRDIAMVFQSYALYP SVR N++FGL+ GLP EI Q V Sbjct: 58 TDGSIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLK-IRGLPKHEIDQEV 116 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E D+L IS L+++KP LSGGQQQRVA+GRA+ R P ++L DEPLSNLDAKLR EMRT Sbjct: 117 ERVADLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRT 176 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+++L L T VYVTHDQ EAMT+ DR+AVL DGELQQ+GTP + Y RP NLFVAGF+ Sbjct: 177 EIKKLHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFM 236 Query: 241 GEPSMNLF-------DGSLSGDTFRGDG--FDYPLSGATRDQLGGASGLTLGIRPEDVTV 291 G P+M+ +G L + DG P+ D++G + LGIRPE +T Sbjct: 237 GSPAMSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVG--KKVILGIRPEHITQ 294 Query: 292 GERRSGQRTFDAE----VVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTT 347 + + +T A+ + V EP G + ++ D T + V G+ Sbjct: 295 PQDQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLND----TNVHCRIDPEHPVTWGETAE 350 Query: 348 VSFPEDAIHLFDGET 362 + F + FD ET Sbjct: 351 LMFDMKKVVFFDPET 365 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: 443 Number of extensions: 25 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: 372 Length adjustment: 30 Effective length of query: 353 Effective length of database: 342 Effective search space: 120726 Effective search space used: 120726 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 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