Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 88.2 bits (217), Expect = 2e-22 Identities = 45/119 (37%), Positives = 74/119 (62%), Gaps = 1/119 (0%) Query: 111 GIRLDI-FTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQ 169 G+RL + FT +LG+ AY GA+++E++R GIL+VP GQ+EA+A+ G T Q + I+VPQ Sbjct: 238 GLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQ 297 Query: 170 TIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYFII 228 +R+I+P + +Q V KN+S+ + VG +L +A + G ++ + Y I Sbjct: 298 ALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAI 356 Score = 46.2 bits (108), Expect = 1e-09 Identities = 20/65 (30%), Positives = 39/65 (60%) Query: 43 AFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFF 102 A + G + +L V + L++ T+ GT+ GV A S ++R +R YV + +N PL++Q+ Sbjct: 81 ALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIV 140 Query: 103 LFYAL 107 ++ + Sbjct: 141 WYFPI 145 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: 222 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: 377 Length adjustment: 27 Effective length of query: 223 Effective length of database: 350 Effective search space: 78050 Effective search space used: 78050 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 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