Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 301 bits (772), Expect = 1e-86 Identities = 172/360 (47%), Positives = 233/360 (64%), Gaps = 27/360 (7%) Query: 1 MAGIKIDKINKFYGTTQA-LFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA +++DK+ K Y + + + +I DGE +V VGPSGCGK+TLLR +AGLE +S G Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 + IG R V + P DRD+AMVFQ+YALYPHMTV EN+ FG+K+ G + R+AEAAR Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +L+LE LD +P LSGGQRQRVA+GRA+V++P VFL DEPLSNLDAKLR+ MRVE+ + Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 H++L ATM+YVTHDQ+EAMT+ +IVVLN G I+Q+ +PM+LY P + FVA F+GSPAM Sbjct: 181 HQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPAM 240 Query: 240 N----VFSSDVGL---------------QDISLDA---SAAFVGCRPEHIEIVPDGDG-H 276 N + D G Q +L+A VG RPE + + D G Sbjct: 241 NLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAGAA 300 Query: 277 IAATVHVKERLGGESLLYLGLKGGG-QIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAG 335 +AA + V E +G E ++L L+ G +V+R+ + G+ + F+ RLH FD G Sbjct: 301 LAAQLEVVEPVGNE--VFLNLRHGELALVSRMPPRELPAPGSTLHFGFAPERLHFFDAKG 358 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: 363 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 338 Length of database: 364 Length adjustment: 29 Effective length of query: 309 Effective length of database: 335 Effective search space: 103515 Effective search space used: 103515 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