Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate BWI76_RS10375 BWI76_RS10375 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__Koxy:BWI76_RS10375 Length = 221 Score = 124 bits (310), Expect = 2e-33 Identities = 72/216 (33%), Positives = 118/216 (54%), Gaps = 5/216 (2%) Query: 32 WKFLDALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELF 91 W F N + G TLE+ +LA ++ T+ G GV+ + T +VE+F Sbjct: 5 WDFSLVWQNLPVLLKGLGVTLELWLLAGIVGTLLGLAVGVVRARGPRFFYPLTSAFVEVF 64 Query: 92 QNVPLVIQIFFLFYALPVL-GIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEA 150 +N P++IQ+ + +YA PVL GI+ F L + Y AY +E+ R+G+ ++ RGQ+E Sbjct: 65 RNTPVLIQLIWFYYAFPVLVGIQFSTFGAAALALTLYTAAYSTEIFRAGLQSIERGQWEG 124 Query: 151 SASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAAD 210 + + G +R II+PQ R +LP +TN+M+ L K TS+ I+ ELM+ ++ Sbjct: 125 AKALGMPPGVMLRRIILPQVFRRMLPALTNRMIELAKVTSLASILTVNELMYQGRLLSST 184 Query: 211 YGNYAPAYIF--AAVLYFIICYPLAYFAKAYENKLK 244 + Y P IF A+LYF++ +P +Y A E + + Sbjct: 185 W--YRPVEIFTVVALLYFVLIWPGSYLAARLERRYR 218 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: 167 Number of extensions: 10 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: 250 Length of database: 221 Length adjustment: 23 Effective length of query: 227 Effective length of database: 198 Effective search space: 44946 Effective search space used: 44946 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: 46 (22.3 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