Align Inositol transport system ATP-binding protein (characterized)
to candidate Ga0059261_0484 Ga0059261_0484 ABC-type multidrug transport system, ATPase component
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Korea:Ga0059261_0484 Length = 245 Score = 100 bits (249), Expect = 3e-26 Identities = 82/256 (32%), Positives = 119/256 (46%), Gaps = 17/256 (6%) Query: 1 MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60 M Q + +Q + +G+ L G+++ V G LLG NGAGKST + + G + Sbjct: 1 MPQDQASVLLQDVSLAYGAQEVLRGLTLSVPAGSITALLGGNGAGKSTTLAALLGFVRAQ 60 Query: 61 KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120 G IL G +DP D IA + +++A+ +S + N L L Sbjct: 61 SGTILVCGVDPG-SDP-DGARRRIAYLPENVALYEHLSATENAEY---------LLALSG 109 Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180 +A R E G+ DQ +G S G RQ VAIA A+ VL+LDEPTS L Sbjct: 110 EQHARRDITEAFAAAGLQEEAWDQRLGGFSKGMRQKVAIAVALLRRVPVLLLDEPTSGLD 169 Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTA-----QRGDI 235 R TA+ A + +VR +G AV+ +TH++ A V DR L G+ +R D+ Sbjct: 170 PRATADFNALVAQVRDRGTAVLMVTHDLLSAADVADRIAFLENGRVTDEVAASGPERFDV 229 Query: 236 SAEELQDMMAGGQELA 251 A + GG+ LA Sbjct: 230 RALHAR-FQVGGEPLA 244 Lambda K H 0.321 0.137 0.395 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: 139 Number of extensions: 6 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: 261 Length of database: 245 Length adjustment: 24 Effective length of query: 237 Effective length of database: 221 Effective search space: 52377 Effective search space used: 52377 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 (21.9 bits) S2: 46 (22.3 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