Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Ac3H11_4787 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4787 Length = 293 Score = 125 bits (315), Expect = 8e-34 Identities = 72/219 (32%), Positives = 118/219 (53%), Gaps = 4/219 (1%) Query: 4 KEALAGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRGVG---SFEFAGLDNFKSVIASNSY 60 + A ++ +P LA +FF P+ ++ F S E+ GLDNFK + Y Sbjct: 8 RSAWLPWVLLAPQLAIISVFFFWPAGQALVQSFQMQDSFGMSTEWVGLDNFKHLFEDPGY 67 Query: 61 RLAVKNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQI 120 + K T F+ + V + +SL+LA+ ++ ++GA ++ +LP + A ++W Sbjct: 68 LASFKTTAFFSILVAAVGIGLSLILAIFADRIIKGAMVYKTALLLPYAVAPAVAGVLWMF 127 Query: 121 TFN-EFGVLNNLLNHFGIAGVEWLNSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDY 179 F+ GV+ +L G LNS ++ ++V+ VWK YN + F AGL SIPK Sbjct: 128 MFSPSLGVVAYMLRQSGFDWNHMLNSDHAMGLIVIAAVWKQISYNFLFFLAGLQSIPKSL 187 Query: 180 YDAASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSF 218 +AA+IDGAG ++ F SI PLL PT FF+ +I+++ +F Sbjct: 188 IEAAAIDGAGPWRRFWSIQFPLLSPTTFFLLVINVVYAF 226 Lambda K H 0.331 0.144 0.444 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: 202 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: 284 Length of database: 293 Length adjustment: 26 Effective length of query: 258 Effective length of database: 267 Effective search space: 68886 Effective search space used: 68886 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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