Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 299 bits (766), Expect = 7e-86 Identities = 161/367 (43%), Positives = 222/367 (60%), Gaps = 14/367 (3%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M +TL K Y GD+ + ++ L IDDGEF V VGPSGCGKST LRM+AGLE Sbjct: 1 MTGVTLAKAVKKY-----GDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEET 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G + + DR + + A DR +AMVFQSYALYPH +V NM FGL+ + G P ++IR++V Sbjct: 56 SSGNIHIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMN-GHPKEKIREKV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E + +L + D L RKP LSGGQ+QRVA+GRAIVR PEVFL DEPLSNLDA+LR +MR Sbjct: 115 AEASRILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRV 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ RL E+G T +YVTHDQ EAMT+ D++ VL G ++QVG+P++ Y P+N FVAGFI Sbjct: 175 EIARLHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G PSMN +G++ GD + + S + LG+RP+ ++V S Sbjct: 235 GSPSMNFLEGTVQGDGVVVPALENRRVATSVALPADGSKVLLGLRPQHLSVTAADSS--- 291 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 +V++ + V ++ G + T G + G + F + ++FDG Sbjct: 292 -----LVLDLRERLGGVSYDYLSTPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFDG 346 Query: 361 ETGDALK 367 T L+ Sbjct: 347 ATEQRLR 353 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: 437 Number of extensions: 24 Number of successful extensions: 2 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: 353 Length adjustment: 30 Effective length of query: 353 Effective length of database: 323 Effective search space: 114019 Effective search space used: 114019 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: 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