Align Inositol transport system ATP-binding protein (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 150 bits (379), Expect = 5e-41 Identities = 82/240 (34%), Positives = 137/240 (57%), Gaps = 4/240 (1%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 ++ ++ I K F V AL VS+++ G +LG+NGAGKST +K +SGV+ KG I + Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 G P+ F + RDA GI +HQ L +IP +S+ N F+G EP P+ L D ++ Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPET---PMGLLDVAKMHK 117 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 + + ++ +N+ P+ V L G++Q V IA+A+ ++V+I+DEPTSA+ ++ Sbjct: 118 EAAQLLHRLKLNV-DPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEI 176 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + I +R +G A+ +I+H + A+ DR+ VL GK + + + ++ E L M G Sbjct: 177 LFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVG 236 Score = 70.5 bits (171), Expect = 7e-17 Identities = 51/206 (24%), Positives = 96/206 (46%), Gaps = 5/206 (2%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAA 82 L ++ ++ GE + G GAG++ ++ + GV +I G+ F P++A+ A Sbjct: 273 LQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDA 332 Query: 83 GIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139 G+A V + ++ M + N + + I L D + + M ++ I Sbjct: 333 GLALVPEDRKQDGLVLCMDLCTNSSL--TVVDSILSGGLLDDKKEKGLAQKYMGELKIKA 390 Query: 140 RGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGV 199 Q V LSGG +Q V +A+ + KVL+LDEPT + + + I ++ +G+ Sbjct: 391 SSHRQLVEKLSGGNQQKVVLAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGL 450 Query: 200 AVVFITHNVRHALAVGDRFTVLNRGK 225 ++ ++ + LAV DR V+ G+ Sbjct: 451 GLIVVSSELPEILAVSDRVLVMAEGR 476 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: 256 Number of extensions: 10 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: 502 Length adjustment: 29 Effective length of query: 232 Effective length of database: 473 Effective search space: 109736 Effective search space used: 109736 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