Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= TCDB::P48245 (273 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 111 bits (277), Expect = 2e-29 Identities = 65/207 (31%), Positives = 116/207 (56%), Gaps = 4/207 (1%) Query: 26 ILPGLWGTLKSAVFSVILALVMGTALGLGRIS-EIRILRWFCAVIIETFRAIPVLILMIF 84 +L G T++ S++L VMG +G+GR++ + R++ C + R P+L+ + Sbjct: 15 LLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFI 74 Query: 85 AYQMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSR 144 + Q+ I+ AF V GL +Y+G+ ++E++R I S+ KGQ EAA ++GMSS Sbjct: 75 LFFGLPQFGILLP---AFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSG 131 Query: 145 QTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALF 204 +++LPQAV M+P L ++ + +K+SAL + +++ G + SV+ L Sbjct: 132 LAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYL 191 Query: 205 VVALIMIVLNFSLTALASRIERQLRAG 231 +A++ +L + T + RIE +LRAG Sbjct: 192 AIAVVYFILTGATTLVLRRIELRLRAG 218 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: 122 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: 273 Length of database: 222 Length adjustment: 24 Effective length of query: 249 Effective length of database: 198 Effective search space: 49302 Effective search space used: 49302 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