Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= TCDB::P48245 (273 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 113 bits (282), Expect = 5e-30 Identities = 71/209 (33%), Positives = 111/209 (53%), Gaps = 7/209 (3%) Query: 18 NSQTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIP 77 N+Q ++ LW TL S + LV+GT L R + ++RW + I R P Sbjct: 48 NAQAFSDGARTTLWLTLISGS----VGLVLGTGAALARTARWAVVRWAASFYIWVIRGTP 103 Query: 78 VLILMIFAYQMFAQYNIVPSSQLA-FAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAA 136 +L+ ++F Y FA +VP L FAA V L + G+ AE +R+G+ ++P+GQ EAA Sbjct: 104 LLVQILFVY--FALPVLVPGLNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAA 161 Query: 137 IALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVN 196 ALG+ + ++ PQA LP L+S V LKDS+L Y IG +E+ G + S Sbjct: 162 KALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSAT 221 Query: 197 RNYLAALFVVALIMIVLNFSLTALASRIE 225 +A L VA+ ++L +T +++ +E Sbjct: 222 FQPIATLSTVAITYLLLTTLVTQISNAVE 250 Lambda K H 0.323 0.136 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: 171 Number of extensions: 11 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: 273 Length of database: 260 Length adjustment: 25 Effective length of query: 248 Effective length of database: 235 Effective search space: 58280 Effective search space used: 58280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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