Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 108 bits (271), Expect = 2e-28 Identities = 65/216 (30%), Positives = 116/216 (53%), Gaps = 8/216 (3%) Query: 42 DAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIF 101 D G TL +S+++ ++ TI G + V SR + +R RIY ++F+ +P V+ I Sbjct: 357 DLLKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVIL 416 Query: 102 FLFYALPVLGIRL---DIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTY 158 + + + L + + +G + + AY+ E+ RSGI +V GQ EAS + GF+Y Sbjct: 417 VVGLGIGPVVKNLTGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSY 476 Query: 159 IQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVL----LIVGGAELMHSADSYAADYGNY 214 Q MR ++VPQ +R +LP + NQ ++LIK++S++ L+ EL A GN Sbjct: 477 RQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGNL 536 Query: 215 APAYIFAAVLYFIICYPLAYFAKAYENKLKKAHLTR 250 +P + A ++Y ++ PL + +++L+ T+ Sbjct: 537 SP-LVAAGLIYLVLTIPLTHLVNYIDHRLRTGRPTQ 571 Lambda K H 0.328 0.143 0.422 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: 329 Number of extensions: 15 Number of successful extensions: 1 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: 250 Length of database: 589 Length adjustment: 30 Effective length of query: 220 Effective length of database: 559 Effective search space: 122980 Effective search space used: 122980 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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