Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PP_1069 PP_1069 glutamate / aspartate ABC transporter - permease subunit
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Putida:PP_1069 Length = 223 Score = 107 bits (266), Expect = 5e-28 Identities = 66/208 (31%), Positives = 111/208 (53%), Gaps = 8/208 (3%) Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLL----FT 281 G ++ L + V ++ + LG +LAL R S ++ +L+ + + R +PL+ ++ Sbjct: 18 GMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWFYLA 77 Query: 282 ASLLLQYFLPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYW 341 +L++ T V+ +F AAY E++R G+ ++ +GQ AA ALG++Y Sbjct: 78 VPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQALGMNYA 137 Query: 342 QAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYW 401 Q RLII+PQA + P ++ I LF+DT+LV VGL D L N RS+ G Sbjct: 138 QTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFL----NSARSNGDIIGRSH 193 Query: 402 EPYIFVALIFFLFNFSMSRYSMYLERKL 429 E IF +++FL +FS S L++++ Sbjct: 194 EFLIFAGVVYFLISFSASWLVKRLQKRI 221 Lambda K H 0.329 0.143 0.457 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: 255 Number of extensions: 17 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: 434 Length of database: 223 Length adjustment: 27 Effective length of query: 407 Effective length of database: 196 Effective search space: 79772 Effective search space used: 79772 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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