Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 274 bits (700), Expect = 3e-78 Identities = 152/363 (41%), Positives = 221/363 (60%), Gaps = 32/363 (8%) Query: 1 MAGIKIDKINKFYG--TTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58 M+ +++ I K Y + L I++DI GEF++ VGPSGCGKSTL+ T+AGLE ++ G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118 I + G+D++T+EP DRD+AMVFQSYALYP M+VREN+ FG+K+ G + + A Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178 +LQ+ +++KP LSGGQ+QRVA+GRA+ + P ++LFDEPLSNLDAKLRV+MR E++ Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPA 238 LH++L T++YVTHDQ+EAMT+AD+I VL G ++Q+G+P ++Y +P + FVA F+GSPA Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 239 MN-----VFSSDVGLQ---------DISLD---------ASAAFVGCRPEHIEIVPD--G 273 M+ V + GLQ + L +G RPEHI D Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300 Query: 274 DGHIAA----TVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLH 329 D + A T+ V E G + + + L + R+ + G L F ++ Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQL-NDTNVHCRIDPEHPVTWGETAELMFDMKKVV 359 Query: 330 QFD 332 FD Sbjct: 360 FFD 362 Lambda K H 0.320 0.139 0.396 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: 393 Number of extensions: 20 Number of successful extensions: 1 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: 338 Length of database: 372 Length adjustment: 29 Effective length of query: 309 Effective length of database: 343 Effective search space: 105987 Effective search space used: 105987 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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