Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate 14935 b0810 glutamine ABC transporter permease protein (NCBI)
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Keio:14935 Length = 219 Score = 95.5 bits (236), Expect = 9e-25 Identities = 64/208 (30%), Positives = 106/208 (50%), Gaps = 9/208 (4%) Query: 26 ILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFA 85 ++ G TL +V + LV+G G R I V IE R P+++ ++F Sbjct: 15 LIEGAKMTLWISVLGLAGGLVIGLLAGFARTFGGWIANHVALVFIEVIRGTPIVVQVMFI 74 Query: 86 Y----QMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGM 141 Y F I P F A V + + +G+ IAEI R + S+ KG +EA +ALG+ Sbjct: 75 YFALPMAFNDLRIDP-----FTAAVVTIMINSGAYIAEITRGAVLSIHKGFREAGLALGL 129 Query: 142 SSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLA 201 S +T ++LP A+ MLP L +Q +I++KD++L IG E+ R G + + N L Sbjct: 130 SRWETIRYVILPLALRRMLPPLGNQWIISIKDTSLFIVIGVAELTRQGQEIIAGNFRALE 189 Query: 202 ALFVVALIMIVLNFSLTALASRIERQLR 229 VA+ +++ L+ + R+ER+++ Sbjct: 190 IWSAVAVFYLIITLVLSFILRRLERRMK 217 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: 163 Number of extensions: 10 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: 219 Length adjustment: 24 Effective length of query: 249 Effective length of database: 195 Effective search space: 48555 Effective search space used: 48555 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: 46 (22.3 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