Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 150 bits (379), Expect = 3e-41 Identities = 87/243 (35%), Positives = 133/243 (54%), Gaps = 18/243 (7%) Query: 2 IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61 +ELKNV+KYYG H +K ++L ++ GE +V +GPSG GKST +R + GLE ++ G+++++ Sbjct: 4 LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63 Query: 62 NLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLA-------PMKLQKKSKKEAEE 114 + ++ ++ AMVFQ + LYPHMTV +N++ A P +Q+K K A++ Sbjct: 64 GRDI---TEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120 Query: 115 TAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEV 174 L + L + P LSGGQ+QRVAI RS+ LFDEP S LD Sbjct: 121 -----LNLTAYLQRT---PKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNT 172 Query: 175 LDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARL 234 + + + T V VTH+ A +ADR++ + DG I + P E + P Sbjct: 173 RVEIASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVAR 232 Query: 235 FLG 237 F+G Sbjct: 233 FIG 235 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: 170 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: 348 Length adjustment: 26 Effective length of query: 216 Effective length of database: 322 Effective search space: 69552 Effective search space used: 69552 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: 48 (23.1 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