Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_009141838.1 HMPREF9452_RS09045 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_000225705.1:WP_009141838.1 Length = 215 Score = 117 bits (292), Expect = 2e-31 Identities = 67/213 (31%), Positives = 117/213 (54%), Gaps = 11/213 (5%) Query: 40 NKDAFINGFIYTLEVSILALLIATIFGTIGGVM---ATSRFKIIRAYTRIYVELFQNVPL 96 N +NGF T+++S+LA++ + I GTI ++ T + + + Y+ELF+ P Sbjct: 8 NMTFIMNGFFKTIQISVLAIIFSLILGTILAMVKQYCTGKLRPLSWIVSAYIELFRCTPN 67 Query: 97 VIQIFFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGF 156 ++ I F+++ + D+F I VL + A ++E+VR G ++P QFEA+ SQGF Sbjct: 68 LLWILFIYFTVK----GSDVF-ISVLAFTIFTSAVMAEIVRGGFNSIPASQFEAARSQGF 122 Query: 157 TYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSAD---SYAADYGN 213 + MRYII+PQT + I+P + +Q +IK++S L V AE M++ + + G Sbjct: 123 GFFATMRYIILPQTFKTIIPALFSQCTTVIKDSSYLAGVNVAEFMYTTKVVMAQTTNLGQ 182 Query: 214 YAPAYIFAAVLYFIICYPLAYFAKAYENKLKKA 246 Y F LYF + + ++ +AY+ ++ A Sbjct: 183 VLMLYGFVFALYFALNFSISLLVRAYQRRVVAA 215 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: 161 Number of extensions: 9 Number of successful extensions: 4 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: 215 Length adjustment: 23 Effective length of query: 227 Effective length of database: 192 Effective search space: 43584 Effective search space used: 43584 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 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