Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_011840329.1 RSPH17029_RS02000 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_000015985.1:WP_011840329.1 Length = 338 Score = 511 bits (1316), Expect = e-149 Identities = 243/338 (71%), Positives = 292/338 (86%) Query: 1 MKKSVFFGSVALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVA 60 M KSVF G++ +A L AG ASA+TLDDVKARG+L CG + GLTGF+ PDANG + GFDV+ Sbjct: 1 MTKSVFLGTLTVAGLAAGLASAATLDDVKARGELNCGVSTGLTGFSLPDANGNWTGFDVS 60 Query: 61 VCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVN 120 +C+AVAAAVLGD KVK+VP TG+TRFTALASGEVD+L RNSTWTFSRDT+L LDFV VN Sbjct: 61 LCRAVAAAVLGDGTKVKFVPTTGQTRFTALASGEVDMLARNSTWTFSRDTDLKLDFVGVN 120 Query: 121 YYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEG 180 YYDGQGFMV K LGV+SAKELDGAT+C+QTGTTTE+NLAD+FK NN++YTPV + +AEG Sbjct: 121 YYDGQGFMVRKDLGVTSAKELDGATVCIQTGTTTELNLADWFKVNNLSYTPVAVETNAEG 180 Query: 181 QQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVR 240 +Q++AAGACD+YTTDASGLA++RA + + +ILPEIISKEPLGP VRHGDN W DIVR Sbjct: 181 EQQYAAGACDAYTTDASGLAATRAAFADPENHIILPEIISKEPLGPAVRHGDNEWADIVR 240 Query: 241 WSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASG 300 W+ AL+AAEEYG+T AN+EE+AA++ NPEI+R+LG++GD+GK I LDND+AKRAI G Sbjct: 241 WTLNALIAAEEYGVTSANMEELAANSPNPEIQRVLGVQGDLGKMIRLDNDWAKRAIAVGG 300 Query: 301 NYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 NYGE+F A IG +T IGLARGLNAQWTQGGL+YAPPFR Sbjct: 301 NYGEIFAATIGEATPIGLARGLNAQWTQGGLLYAPPFR 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: 445 Number of extensions: 10 Number of successful extensions: 1 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 Apr 10 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