Align Inositol transport system ATP-binding protein (characterized)
to candidate 3607868 Dshi_1276 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Dino:3607868 Length = 264 Score = 454 bits (1169), Expect = e-133 Identities = 220/256 (85%), Positives = 246/256 (96%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 P+I+M+ IEKHFG+VIALAGVS+D+FPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG+I+ Sbjct: 9 PIIQMKNIEKHFGAVIALAGVSIDIFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGEII 68 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 FEG+P+HF DPRDA+ AGIATVHQHLAMIPLMSVSRNFFMGNEP++KI + D ++A+ Sbjct: 69 FEGRPMHFEDPRDAMEAGIATVHQHLAMIPLMSVSRNFFMGNEPVKKIAGINFLDREFAD 128 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 R+TMEEMRKMGINLRGPDQAVGTLSGGERQTVAI+RAV+FGAKVLILDEPTSALGVRQT+ Sbjct: 129 RVTMEEMRKMGINLRGPDQAVGTLSGGERQTVAISRAVYFGAKVLILDEPTSALGVRQTS 188 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 NVLATIDKVRKQGVAVVFITHNVRHA+AVGDRFTVLNRG+TLGTA+RG+I+ EELQDMMA Sbjct: 189 NVLATIDKVRKQGVAVVFITHNVRHAMAVGDRFTVLNRGQTLGTAERGEITPEELQDMMA 248 Query: 246 GGQELATLEGSLGGTV 261 GGQELATLEGSLGGTV Sbjct: 249 GGQELATLEGSLGGTV 264 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: 376 Number of extensions: 7 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: 261 Length of database: 264 Length adjustment: 25 Effective length of query: 236 Effective length of database: 239 Effective search space: 56404 Effective search space used: 56404 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: 47 (22.7 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