Align Inositol transport system ATP-binding protein (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 156 bits (395), Expect = 7e-43 Identities = 88/244 (36%), Positives = 138/244 (56%), Gaps = 5/244 (2%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 M P++R+ GI K FG ++A +S+++ GE LLG+NGAGKST + + G + G Sbjct: 1 MPTPILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAG 60 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHD 122 + +GQPL PR A+ AGI VHQH + +SV N +G +P+ + +L H Sbjct: 61 TVEVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQ---WRLDGHA 117 Query: 123 YANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182 ++ + + G+ +R P VG LS GERQ V I +A++ GA+VLILDEPT+ L Sbjct: 118 ARGKV-LALAERFGLAVR-PQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPH 175 Query: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 + + +T+ ++ +G++V+FI+H + L V DR VL GK + + EL + Sbjct: 176 EAETLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAE 235 Query: 243 MMAG 246 +M G Sbjct: 236 LMVG 239 Score = 65.5 bits (158), Expect = 2e-15 Identities = 56/232 (24%), Positives = 102/232 (43%), Gaps = 9/232 (3%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAA 82 L VS+ V GE + G +G G++ + SG+ + ++G I G+P+ A PR I A Sbjct: 282 LREVSLQVRAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMS-AKPRAWIGA 340 Query: 83 GIATVHQH---LAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139 G+A V + + ++ ++V N + + A R + + + + Sbjct: 341 GVARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRT 400 Query: 140 RGPDQAVGTLSGGERQTVAIARAVHF-----GAKVLILDEPTSALGVRQTANVLATIDKV 194 G D T+SGG Q + + RA+ ++++ +PT L + A V A + Sbjct: 401 AGIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDA 460 Query: 195 RKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 ++G AV+ I+ ++ A+ DR V++ G + EL MAG Sbjct: 461 AREGAAVLLISEDLDELHALADRIAVMHAGHLTEARPTAAWTLGELGLAMAG 512 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: 339 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 261 Length of database: 530 Length adjustment: 30 Effective length of query: 231 Effective length of database: 500 Effective search space: 115500 Effective search space used: 115500 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: 49 (23.5 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