Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 77.4 bits (189), Expect = 4e-19 Identities = 35/81 (43%), Positives = 56/81 (69%) Query: 121 VLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTN 180 + + Y +++E +RSGI AVP+GQ EA+ S G + +QQ+R +I+PQ +RI +P + N Sbjct: 256 LFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIPSIIN 315 Query: 181 QMVNLIKNTSVLLIVGGAELM 201 Q +NLIKN+S+ +G EL+ Sbjct: 316 QYLNLIKNSSLAAAIGYPELV 336 Score = 40.0 bits (92), Expect = 7e-08 Identities = 20/71 (28%), Positives = 37/71 (52%) Query: 34 FLDALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQN 93 F A + F G + TL VS ++ +++ G + G+ S +I Y+E F+N Sbjct: 65 FTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRN 124 Query: 94 VPLVIQIFFLF 104 +P+++QI F + Sbjct: 125 IPVLLQILFWY 135 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: 238 Number of extensions: 11 Number of successful extensions: 2 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: 384 Length adjustment: 27 Effective length of query: 223 Effective length of database: 357 Effective search space: 79611 Effective search space used: 79611 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: 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