Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate BWI76_RS05955 BWI76_RS05955 ABC transporter
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Koxy:BWI76_RS05955 Length = 272 Score = 228 bits (582), Expect = 7e-65 Identities = 124/241 (51%), Positives = 159/241 (65%), Gaps = 3/241 (1%) Query: 2 IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61 IE ++V K YG H VL +NL V+ GE + I+GPSGSGKST IR +N LE +S GE++++ Sbjct: 24 IEFRDVAKSYGDHRVLNGVNLQVEPGEVVAILGPSGSGKSTLIRLINQLESLSGGEILID 83 Query: 62 NLVLNHK--NKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 + + R VFQ FNLY H+T +N+TLA ++ K A E + Sbjct: 84 GKPTRQLTGSALRQLRSRVGFVFQQFNLYAHLTAQENITLALERVHGWGKSAARERSLAL 143 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L VGL DKA PA LSGGQQQRVAIAR+L + ILFDEPTSALDPE I EVL VMK Sbjct: 144 LSQVGLADKAGQMPAQLSGGQQQRVAIARALASSPQIILFDEPTSALDPEMIGEVLQVMK 203 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239 ++H S TMVVVTHEM FA+E+ADR++F++ G I+E P+EFF+ P+ R R FL K+ Sbjct: 204 TLAH-SGITMVVVTHEMQFAREIADRVVFIDGGDILEVAPPAEFFARPQHARTRRFLQKV 262 Query: 240 L 240 L Sbjct: 263 L 263 Lambda K H 0.317 0.133 0.372 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: 147 Number of extensions: 5 Number of successful extensions: 3 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: 242 Length of database: 272 Length adjustment: 24 Effective length of query: 218 Effective length of database: 248 Effective search space: 54064 Effective search space used: 54064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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