Align Inositol transport system ATP-binding protein (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 155 bits (391), Expect = 2e-42 Identities = 80/243 (32%), Positives = 143/243 (58%), Gaps = 6/243 (2%) Query: 5 QPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDI 64 + L++++GI+K F V AL+G +++V+PG L+G+NGAGKST +K ++G++ G + Sbjct: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 Query: 65 LFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYA 124 L+ G+ F P+ + AGI +HQ L +IP ++++ N F+G E + + G + D+ Sbjct: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKI-----DWK 116 Query: 125 NRITMEEMRKMGINLR-GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183 + +NLR D+ VG LS G++Q V IA+ + F +KV+I+DEPT AL + Sbjct: 117 TMYAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTE 176 Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 T ++ I +++ QG +V+I+H ++ + D TV G+ + + ++ + L +M Sbjct: 177 TESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEM 236 Query: 244 MAG 246 M G Sbjct: 237 MVG 239 Score = 86.7 bits (213), Expect = 9e-22 Identities = 64/226 (28%), Positives = 103/226 (45%), Gaps = 8/226 (3%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 VS + GE + G GAG++ +K + G T G + +G + P+D +A GI Sbjct: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIV 330 Query: 86 TVHQHL---AMIPLMSVSRNFFMGNEPI--RKIGPLKLFDHDYANRITMEEMRKMGINLR 140 + + ++ MSV N + R G LK D A + +R + Sbjct: 331 YISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQA---VSDFIRLFNVKTP 387 Query: 141 GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVA 200 +QA+G LSGG +Q VAIAR + KVLILDEPT + V + I++ + G++ Sbjct: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447 Query: 201 VVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 ++ ++ + L + DR V++ G G R + E L G Sbjct: 448 IILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVG 493 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: 298 Number of extensions: 18 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: 501 Length adjustment: 29 Effective length of query: 232 Effective length of database: 472 Effective search space: 109504 Effective search space used: 109504 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