Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 92.0 bits (227), Expect = 2e-23 Identities = 72/225 (32%), Positives = 107/225 (47%), Gaps = 10/225 (4%) Query: 172 LFTALAPKLGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLAL 231 + TA P+ +V+A+ + A + L S LP + G L Sbjct: 1 MLTAFWPQRWSRQQRSNATLVSAVILMVLALALLGQLLSFLPEPIGSNAQAFSDGARTTL 60 Query: 232 VIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYF-- 289 + + + V L LG AL R + +V+ + I +RG PL+ +L YF Sbjct: 61 WLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLV-----QILFVYFAL 115 Query: 290 --LPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLI 347 L PG N V+ + L AY AE IR GL A+PRGQ EAA ALGL + Sbjct: 116 PVLVPGLNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGLGRMHVFFDV 175 Query: 348 IMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRS 392 + PQA KIS+P +VS+F+ L KD++L +G+ + L + N ++S Sbjct: 176 VFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVE-LTNVGNRIQS 219 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: 328 Number of extensions: 19 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: 260 Length adjustment: 28 Effective length of query: 406 Effective length of database: 232 Effective search space: 94192 Effective search space used: 94192 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: 49 (23.5 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