Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 314 bits (804), Expect = 3e-90 Identities = 178/372 (47%), Positives = 233/372 (62%), Gaps = 35/372 (9%) Query: 1 MAGIKIDKINKFYGT-TQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA I + + K YG + D++L+I + EF VF+GPSGCGKSTLLR +AGLE ++ G Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 + IGG+ + V A R +AMVFQSYAL+PHMTV ENM FG+K+ D ++ EAAR Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +LQLE L+R+P LSGGQRQRVAIGRAIV+ P VFLFDEPLSNLDA LR Q R+E+ L Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HKQLG-ATMIYVTHDQVEAMTMADKIVVLNRGR-------IEQVGSPMDLYHKPNSRFVA 231 HKQ A+++YVTHDQ+EAMT+ADKIV+L+ G+ I Q+G+P++LYH+P SRFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 232 EFIGSPAMNVFSSDVGLQD-----ISLD-----------------ASAAFVGCRPEHIEI 269 FIGSP MN + D ++LD + A +G RPEH+E Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300 Query: 270 VPDGDGH----IAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSR 325 H ++ TV + E+LG S ++L GG ++A+ GD G +LR R Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGVALIAKAPGDTRLAPGDRANLRVPR 360 Query: 326 HRLHQFDEAGRA 337 H H F E G A Sbjct: 361 HATHLFTEDGFA 372 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: 390 Number of extensions: 19 Number of successful extensions: 5 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: 383 Length adjustment: 29 Effective length of query: 309 Effective length of database: 354 Effective search space: 109386 Effective search space used: 109386 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