Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 3606888 Dshi_0318 cationic amino acid ABC transporter, periplasmic binding protein (RefSeq)
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__Dino:3606888 Length = 338 Score = 461 bits (1187), Expect = e-135 Identities = 219/338 (64%), Positives = 274/338 (81%) Query: 1 MKKSVFFGSVALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVA 60 MKKSV FG++A A L A A+A TL++V+ARG + CG + GL GFA+ DANG +QGFDVA Sbjct: 1 MKKSVLFGALAAAGLAATGAAADTLEEVQARGAVNCGISTGLVGFASQDANGEWQGFDVA 60 Query: 61 VCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVN 120 VC+AVAAAV GDP V + P+T + RF L SGE+D+L RN+TWTFSRD +L L+F +N Sbjct: 61 VCRAVAAAVFGDPTAVNFNPVTNQVRFEVLNSGEIDMLARNTTWTFSRDVDLKLEFTGIN 120 Query: 121 YYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEG 180 YYDGQGFMV K+LGVSSA ELDGAT+C+Q GTTTE+NLADFF+ANN+++ PV I+ +E Sbjct: 121 YYDGQGFMVPKALGVSSATELDGATVCIQKGTTTELNLADFFRANNISFEPVPISTASEA 180 Query: 181 QQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVR 240 QQ++ AGACD YTTDASGLA++RA+ + + V+LPEIISKEPLGP+VRHGDN WGDIVR Sbjct: 181 QQQYLAGACDVYTTDASGLAATRASFESPDEHVVLPEIISKEPLGPLVRHGDNEWGDIVR 240 Query: 241 WSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASG 300 W+ AL+AAEE G+T AN+ E+AA T NPEI RLLG EG++G+++GL D+A I A G Sbjct: 241 WTLNALIAAEELGVTSANVAELAAGTDNPEINRLLGTEGNLGEQLGLSADWAVNVIKAGG 300 Query: 301 NYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 NYGE+FE +IG +T IGLARGLNAQWT+GGL+YAPPFR Sbjct: 301 NYGEIFETHIGENTPIGLARGLNAQWTEGGLLYAPPFR 338 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: 401 Number of extensions: 15 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: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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