Align Inositol transport system ATP-binding protein (characterized)
to candidate BPHYT_RS13905 BPHYT_RS13905 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__BFirm:BPHYT_RS13905 Length = 258 Score = 289 bits (739), Expect = 5e-83 Identities = 140/254 (55%), Positives = 194/254 (76%), Gaps = 1/254 (0%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 ++ ++ + K+FG VIAL+GV++ + GE HCLLGDNGAGKST IKT++GVH+P+ G L Sbjct: 2 ILALENVNKYFGKVIALSGVTLRLKRGEVHCLLGDNGAGKSTLIKTLAGVHQPSSGQYLV 61 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKI-GPLKLFDHDYAN 125 +G+P+ F P+DA+ GIATV+Q LA++PL+SV+RNFFMG EP +K+ G L + D + + Sbjct: 62 DGKPVLFESPKDALDLGIATVYQDLALVPLLSVARNFFMGREPQKKLFGFLSVMDLETSA 121 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 +++ +MGIN+R Q +GT+SGGE+Q +AIARA+HFGA+VLILDEPT+ALGV+Q+ Sbjct: 122 TTARDKLAEMGINVRDAHQPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVKQSF 181 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245 NVL I K R +G++V+FITHNV HA +GD FTVLNRGK+LGT + IS +E+ DMMA Sbjct: 182 NVLKLIHKARAKGISVIFITHNVHHAYPIGDSFTVLNRGKSLGTFTKETISKDEVLDMMA 241 Query: 246 GGQELATLEGSLGG 259 GG E+ + G L G Sbjct: 242 GGAEMQKMIGELEG 255 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: 261 Number of extensions: 10 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: 258 Length adjustment: 24 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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