Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate RR42_RS12965 RR42_RS12965 glycerol-3-phosphate transporter permease
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__Cup4G11:RR42_RS12965 Length = 293 Score = 133 bits (335), Expect = 4e-36 Identities = 77/214 (35%), Positives = 120/214 (56%), Gaps = 6/214 (2%) Query: 10 YLFSSPYLAGFLIFFAIPSAMSVYYCFTR----GVGSFEFAGLDNFKSVIASNSYRLAVK 65 YL P +A LIFF P+ ++Y R G+ +F GL+NF+ + + Y A + Sbjct: 14 YLLVLPQMAVTLIFFFWPAGQALYQSVLRQDAFGI-DLQFVGLENFRDLFSDAQYLNAFR 72 Query: 66 NTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQITFNE- 124 T +F V + VSL+LA ++ +RGA ++M + P + A ++W FN Sbjct: 73 VTGVFAVGVTLVGLTVSLMLAYFADRVVRGASGYKMLLIWPYAVAPAVAGVLWMFMFNPT 132 Query: 125 FGVLNNLLNHFGIAGVEWLNSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYDAAS 184 GV++ L+ FG+ LNS ++ ++VL+ WK YN + F AGL SIPK +AA+ Sbjct: 133 LGVVSYALHRFGVDWNFLLNSNQAMLLVVLIAAWKQISYNFLFFLAGLQSIPKSLIEAAA 192 Query: 185 IDGAGGFKCFTSITLPLLVPTIFFVFIISIINSF 218 IDGAG ++ F SI PLL PT FF+ +I+++ +F Sbjct: 193 IDGAGPWRRFWSIIFPLLSPTTFFLMVINVVYAF 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: 207 Number of extensions: 11 Number of successful extensions: 3 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