Align Inositol transport system ATP-binding protein (characterized)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS22465 Length = 518 Score = 158 bits (399), Expect = 3e-43 Identities = 93/246 (37%), Positives = 140/246 (56%), Gaps = 5/246 (2%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGV--HKPT 60 MS+ L+ M+GI K FG V AL G+ + + PGEC L G+NGAGKST +K +SGV H Sbjct: 1 MSEYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTW 60 Query: 61 KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120 +G+IL++G+PL RD AAGI +HQ L ++P +SV+ N FMG+E G + Sbjct: 61 EGEILWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGRMNYPA 120 Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180 M E+ IN+ P V GG +Q V IA+A++ A++LILDEP+S+L Sbjct: 121 MYRRAEELMRELNMPDINVALP---VSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLT 177 Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 + +L I ++ +GVA V+I+H + V D +V+ GK + T ++ +++ Sbjct: 178 ASEIGVLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKI 237 Query: 241 QDMMAG 246 M G Sbjct: 238 ITQMVG 243 Score = 87.8 bits (216), Expect = 4e-22 Identities = 57/217 (26%), Positives = 103/217 (47%), Gaps = 6/217 (2%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT-KGDILFEGQPLHFADPRDAIAAGI 84 VS V GE + G GAG++ + + G ++ +G +L EG+P + P +I G+ Sbjct: 283 VSFSVRRGEILGIAGLVGAGRTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGL 342 Query: 85 ATV---HQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRG 141 V +H ++P + V +N + + + D + +E+ +M + Sbjct: 343 CMVPEDRKHHGIVPDLDVGQNITL--TVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTAT 400 Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201 P + +LSGG +Q +A+ + KVLILDEPT + V A + I ++ K G+A+ Sbjct: 401 PFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAI 460 Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238 + ++ + L V DR V+ G+ G ++S E Sbjct: 461 IMVSSELAEVLGVSDRVLVIGEGRLRGDFVNDNLSQE 497 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: 317 Number of extensions: 12 Number of successful extensions: 4 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: 518 Length adjustment: 30 Effective length of query: 231 Effective length of database: 488 Effective search space: 112728 Effective search space used: 112728 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