Align Inositol transport system ATP-binding protein (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 155 bits (393), Expect = 1e-42 Identities = 84/244 (34%), Positives = 142/244 (58%), Gaps = 1/244 (0%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 M+ P I M GI K FG V AL V++ V+PGE H LLG+NGAGKST +K +SG+H+PTKG Sbjct: 1 MATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKG 60 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHD 122 I + D + A GI ++Q L++I ++V N ++G +KI + + D Sbjct: 61 TITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWR 120 Query: 123 YANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182 + ++G+ + D+ V LS +Q + IA+ + AKV+I+DEPTS+L + Sbjct: 121 EMRVRAAMMLLRVGLKV-DLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNK 179 Query: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 + + ++++RK+G A+V+I+H + + DR+TV+ G ++ + D+S +++ Sbjct: 180 EVDYLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVR 239 Query: 243 MMAG 246 +M G Sbjct: 240 LMVG 243 Score = 71.6 bits (174), Expect = 3e-17 Identities = 57/226 (25%), Positives = 104/226 (46%), Gaps = 16/226 (7%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 +S V GE G G+G++ + + GV K G+I G+ + P DA+ G+A Sbjct: 282 ISFSVCRGEILGFAGLVGSGRTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMA 341 Query: 86 TVHQ---------HLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKM- 135 + + + ++ M++SR+ G G + LF H+ + T E R++ Sbjct: 342 YITESRRDNGFFPNFSIAQNMAISRSLKDGGYK----GAMGLF-HEVDEQRTAENQRELL 396 Query: 136 GINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVR 195 + +Q + LSGG +Q V I++ + +V+I DEPT + V A + + ++ Sbjct: 397 ALKCHSVNQNITELSGGNQQKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLA 456 Query: 196 KQGVAVVFITHNVRHALAVGDRFTVLNRGK-TLGTAQRGDISAEEL 240 G ++ ++ + + V DR V G+ T R D+S EE+ Sbjct: 457 DDGKVILMVSSELPEIITVCDRIAVFCEGRLTQILTNRDDMSEEEI 502 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: 290 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: 510 Length adjustment: 29 Effective length of query: 232 Effective length of database: 481 Effective search space: 111592 Effective search space used: 111592 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