Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS12120 HSERO_RS12120 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS12120 Length = 266 Score = 283 bits (724), Expect = 3e-81 Identities = 135/253 (53%), Positives = 189/253 (74%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 ++ + + K FG VIAL VS+ + GE HCLLGDNGAGKST IK ++GVH+ + G L Sbjct: 11 ILELDQVSKFFGPVIALQNVSLRLRRGEVHCLLGDNGAGKSTLIKLLAGVHQASSGQYLV 70 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 +G+P+ F P++A+ G+ATV+Q LA++PL+SV+RNFF+G EP+RK+ + + D + A R Sbjct: 71 DGKPVRFESPKEALDVGVATVYQDLALVPLLSVARNFFLGREPVRKLFGVTVMDMELAAR 130 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 E++ +MGI +R +GT+SGGE+Q +AIARA+HFGA+VLILDEPT+ALGV+Q+ N Sbjct: 131 TAKEKLAEMGIMVRDAHHPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVKQSFN 190 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 VL I + R++G++V+FITHNV HA +GD FT+LNRGK+LG+ + IS EE+ DMMAG Sbjct: 191 VLKLIHRARERGISVIFITHNVHHAYPIGDTFTLLNRGKSLGSFAKDRISKEEVLDMMAG 250 Query: 247 GQELATLEGSLGG 259 G E+ TL G L G Sbjct: 251 GAEMQTLMGQLEG 263 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: 252 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: 266 Length adjustment: 25 Effective length of query: 236 Effective length of database: 241 Effective search space: 56876 Effective search space used: 56876 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