Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::A1VZQ3 (250 letters) >MicrobesOnline__882:206177 Length = 596 Score = 127 bits (319), Expect = 5e-34 Identities = 72/231 (31%), Positives = 130/231 (56%), Gaps = 6/231 (2%) Query: 17 SWGLYDENSISPFAVWKFLDAL-DNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATS 75 +WG+ +N + +W F + D + G Y+L ++++A+ ++ G + G+ TS Sbjct: 359 NWGVIADN-LRTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSFFIGLVVGIGRTS 417 Query: 76 RFKIIRAYTRIYVELFQNVPLVIQIFFLFYALPVL-GIRLDIFTIGVLGVGAYHGAYVSE 134 +I R +Y+EL + PL+I IF++++ +PVL ++F + + + GAY++E Sbjct: 418 DNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLFNTFFNVFWSATIALTLFTGAYLAE 477 Query: 135 VVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLI 194 +VR+GI +P GQ EA+ S G T++Q MR II+PQ ++ ++P + Q + + K+TS+ + Sbjct: 478 IVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIPAIVGQFIAIFKDTSLAFV 537 Query: 195 VGGAELMHSADSYAADYGNYAPAYIFAAV--LYFIICYPLAYFAKAYENKL 243 +G EL A Y P I+ V LYFI C+ ++ +A E +L Sbjct: 538 LGVLELTFVAQGINNRLMVY-PMEIYGTVAFLYFICCWSMSVYAARLERRL 587 Score = 117 bits (292), Expect = 7e-31 Identities = 63/209 (30%), Positives = 114/209 (54%), Gaps = 9/209 (4%) Query: 45 INGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLF 104 + G T+ +S+++ +A GT+ G+ S F +R VE F+N PL++Q+FF + Sbjct: 58 LKGLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWY 117 Query: 105 YALPVL---GIRLDIFT------IGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQG 155 +A P + IR +FT +G+ Y A+++EV+R+G+ ++P+G EA+ S G Sbjct: 118 FAFPAILPENIRELLFTGNFEFWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSG 177 Query: 156 FTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYA 215 Y+Q +R II+P R I+PP+ ++ +N +KN+S+ ++VG AEL + + Sbjct: 178 LNYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWQSQQVESLTFKGF 237 Query: 216 PAYIFAAVLYFIICYPLAYFAKAYENKLK 244 A A VLY + +++ K++ Sbjct: 238 EATSAATVLYLSLSLLISFILNGVNGKMR 266 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: 368 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 250 Length of database: 596 Length adjustment: 30 Effective length of query: 220 Effective length of database: 566 Effective search space: 124520 Effective search space used: 124520 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 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