Align Inositol transport system ATP-binding protein (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 103 bits (257), Expect = 5e-27 Identities = 71/226 (31%), Positives = 115/226 (50%), Gaps = 22/226 (9%) Query: 8 IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67 I ++ I K FG+ +AL VS+ + GE LLG +G GK+T ++ ++G+ +G ++FE Sbjct: 3 IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62 Query: 68 GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127 G R+ + V QH A+ M+V N G ++ P K R Sbjct: 63 GSEATHLHARE---RQVGFVFQHYALFRHMNVFENVAFG----LRVKPRK-------ERP 108 Query: 128 TMEEMRKMGINLRG-------PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180 E+RK ++L D+ LSGG+RQ +A+ARA+ KVL+LDEP AL Sbjct: 109 CESEIRKRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALD 168 Query: 181 VRQTANVLATIDKVR-KQGVAVVFITHNVRHALAVGDRFTVLNRGK 225 + + + ++ + ++ VF+TH+ AL V DR V+N+G+ Sbjct: 169 TKVRKELRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGR 214 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: 218 Number of extensions: 12 Number of successful extensions: 3 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: 360 Length adjustment: 27 Effective length of query: 234 Effective length of database: 333 Effective search space: 77922 Effective search space used: 77922 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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