Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__Marino:GFF2246 Length = 347 Score = 363 bits (932), Expect = e-105 Identities = 177/339 (52%), Positives = 236/339 (69%), Gaps = 5/339 (1%) Query: 3 KSVFFGSVALAA---LVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDV 59 KS+ G +ALA GA +A+TL++VK +G L CG GL GF+ PD G + G DV Sbjct: 11 KSIALG-IALAVGTFSATGAMAATTLENVKEKGHLQCGVTSGLPGFSQPDEKGNWTGIDV 69 Query: 60 AVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAV 119 C+AVAAA+ GD V++ PLT + RFTAL SGE+D+L RN+TWT +RD L L+F V Sbjct: 70 DTCRAVAAAIFGDANAVEFTPLTAKERFTALQSGEIDMLSRNTTWTLTRDASLGLNFAGV 129 Query: 120 NYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAE 179 NYYDGQGF++NK +GV A +LDGATIC+Q GTTTE+NL+D+F+A M + P+ + Sbjct: 130 NYYDGQGFLINKGIGVDDATQLDGATICIQAGTTTELNLSDYFRAKGMEFKPIVFDTSEQ 189 Query: 180 GQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIV 239 Q FAAG CD T+D S LA+ R+ L + + ILP ISKEPLGPVVR GD+ W +IV Sbjct: 190 TVQGFAAGRCDVLTSDRSQLAALRSKLSDPSSAKILPNTISKEPLGPVVRQGDDQWFNIV 249 Query: 240 RWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILAS 299 +W +A + AEE G+T AN +++ S NP I+RLLG +GDMG K+GL +DF +A+ Sbjct: 250 KWVLFAQINAEELGVTSANADDMLKS-DNPNIQRLLGTDGDMGAKLGLPDDFGYQAVKLV 308 Query: 300 GNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 GNYGE+++ N+G T +GL RG+NA WT+GG+MYAPP R Sbjct: 309 GNYGEMYDRNVGPDTPLGLDRGINALWTEGGIMYAPPVR 347 Lambda K H 0.316 0.132 0.384 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: 367 Number of extensions: 8 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: 338 Length of database: 347 Length adjustment: 29 Effective length of query: 309 Effective length of database: 318 Effective search space: 98262 Effective search space used: 98262 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 (21.6 bits) S2: 49 (23.5 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