Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011373656.1 SUDEN_RS10595 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000012965.1:WP_011373656.1 Length = 236 Score = 134 bits (337), Expect = 2e-36 Identities = 86/223 (38%), Positives = 125/223 (56%), Gaps = 13/223 (5%) Query: 1 MIELKNVNKYYG----THHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 +I L V K YG T + L+ +NL +K GE + I+GPSGSGKST + + L+ +SSG Sbjct: 9 VISLHKVVKSYGSAEATTYALRGVNLEIKRGEFVAIMGPSGSGKSTAMNIIGCLDTLSSG 68 Query: 57 E-----VVVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKE 111 + V + L L+ + + R Y +FQ FNL T ++N+ L P+ + ++ Sbjct: 69 DYLFGGVDIQKLSLDQRTLLR--RNYIGFIFQGFNLLGKTTAIENVEL-PLLYRGFPARQ 125 Query: 112 AEETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETI 171 E A L+ VGL A+ PA LSGGQQQRVAIAR++ T +L DEPT LD Sbjct: 126 RSEMAMNALRSVGLEQVAHHTPAELSGGQQQRVAIARAIVTDPFILLADEPTGNLDTAKS 185 Query: 172 QEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAI 214 +E+++++ + + T+V+VTHE A A RII DG I Sbjct: 186 REIMELLSSFNKEKGLTIVMVTHENEMA-SYASRIIRFRDGKI 227 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: 111 Number of extensions: 8 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: 236 Length adjustment: 23 Effective length of query: 219 Effective length of database: 213 Effective search space: 46647 Effective search space used: 46647 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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