Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 115 bits (289), Expect = 6e-31 Identities = 62/200 (31%), Positives = 112/200 (56%), Gaps = 3/200 (1%) Query: 51 TLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYALP-V 109 TL ++++A+++A + ++ V R ++ +++ F+ PL++Q+F +Y LP V Sbjct: 23 TLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQLFLFYYGLPQV 82 Query: 110 LGIRLDI--FTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIV 167 L + I + ++G+ + AY++E +R+ IL V R Q+EA+ S G T Q MR I++ Sbjct: 83 LSVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQWEAAQSIGMTRGQMMRRIVL 142 Query: 168 PQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYFI 227 PQ RI P + N +++IK TS+ +G E+M + AA Y A++ AV+Y+I Sbjct: 143 PQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKEAAGSFLYFEAFLVVAVIYWI 202 Query: 228 ICYPLAYFAKAYENKLKKAH 247 + L+ + E L KA+ Sbjct: 203 LVEALSLVQRRLETHLNKAY 222 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: 169 Number of extensions: 11 Number of successful extensions: 2 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: 224 Length adjustment: 23 Effective length of query: 227 Effective length of database: 201 Effective search space: 45627 Effective search space used: 45627 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 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