Align Inositol transport system ATP-binding protein (characterized)
to candidate BPHYT_RS22735 BPHYT_RS22735 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__BFirm:BPHYT_RS22735 Length = 265 Score = 189 bits (481), Expect = 4e-53 Identities = 101/251 (40%), Positives = 149/251 (59%), Gaps = 3/251 (1%) Query: 2 SMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 S + P+++ +G+ K +G+V AL G +V PGE ++GDNGAGKS+ IK +SG P + Sbjct: 8 SSAMPVLQARGLIKRYGNVTALDGCDFEVMPGEIMAVIGDNGAGKSSLIKALSGATVPDE 67 Query: 62 GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIR---KIGPLKL 118 G+IL +G+P+ F P DA A GI TV+Q LA+ P MS++ N F+ E ++ + K+ Sbjct: 68 GEILLDGKPVKFRSPLDARAQGIETVYQELAVAPAMSIAENLFLARELLKPGWRGSIFKM 127 Query: 119 FDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178 D M+ + I +R QAV TLSGG+RQ VA+AR+ F V+ILDEPT+A Sbjct: 128 IDKRRMLDEATAHMKDLQIGIRSMRQAVETLSGGQRQGVAVARSAAFARHVVILDEPTAA 187 Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238 LGV++ VL I +VR +G+ V+ I+HN+ H + DR + G+ R DI Sbjct: 188 LGVKEGNMVLELIRRVRDRGLPVILISHNMPHVFEIADRIHIQRLGRRAALVNRADIHMS 247 Query: 239 ELQDMMAGGQE 249 E +M G +E Sbjct: 248 EAVAIMTGAKE 258 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: 172 Number of extensions: 11 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: 265 Length adjustment: 25 Effective length of query: 236 Effective length of database: 240 Effective search space: 56640 Effective search space used: 56640 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