Align Inositol transport system ATP-binding protein (characterized)
to candidate Ac3H11_3037 Fructose ABC transporter, ATP-binding component FrcA
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3037 Length = 268 Score = 176 bits (446), Expect = 5e-49 Identities = 96/251 (38%), Positives = 147/251 (58%), Gaps = 5/251 (1%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 +++ +G+ K +G V AL G ++ GE ++GDNGAGKS+ IK +SG P +G+IL Sbjct: 13 VMQAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKALSGATVPDEGEILL 72 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIG----PLKLFDHD 122 +GQ + F P +A AGI TV+Q LA+ P M+++ N F+G E +R+ G L++ D Sbjct: 73 DGQRIQFKSPIEARRAGIETVYQDLAVAPAMTIAENLFLGRE-LRRPGLLGTALRMLDKK 131 Query: 123 YANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182 ++ M ++ + +R QAV TLSGG+RQ VA+ARA F V+I+DEPT+ALGV+ Sbjct: 132 KMLEESVARMAELKVGIRSMTQAVETLSGGQRQCVAVARAAAFARHVVIMDEPTAALGVK 191 Query: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 + VL I +VR +G+ V+ I+HN+ H + DR + GK IS + Sbjct: 192 EGNMVLELIRRVRDKGLPVILISHNMPHVFEIADRIHIARLGKRAAVVNPKKISMSDTVA 251 Query: 243 MMAGGQELATL 253 +M G + L Sbjct: 252 VMTGAMAASDL 262 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: 166 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 261 Length of database: 268 Length adjustment: 25 Effective length of query: 236 Effective length of database: 243 Effective search space: 57348 Effective search space used: 57348 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: 47 (22.7 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