Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_002117405.1:WP_245299991.1 Length = 350 Score = 256 bits (655), Expect = 5e-73 Identities = 136/340 (40%), Positives = 205/340 (60%), Gaps = 10/340 (2%) Query: 7 FGSVALAALVAG---AASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCK 63 FG VA A +A + ++STL +++ RG ++CG+ GFA D G + GFD+ C+ Sbjct: 13 FGLVAGAPRLAAQPESKASSTLQEIRRRGVVVCGATAPAPGFAVMDEAGSWSGFDIDFCR 72 Query: 64 AVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYD 123 A+A A L DP K++ L + R AL SG+VDVL+ + WT +R+ L + A+++Y Sbjct: 73 ALAVAALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWTEAREAGHQLLYGAISFYG 132 Query: 124 GQGFMVNKSLGVSSAKELDGA-----TICVQTGTTTEMNLADFFKANNMTYTPVNIADDA 178 GQGF+ ++ G + + GA +CVQ G ++E+NLA F++ + + Y PV Sbjct: 133 GQGFLGRRAWG-PTGEPWRGAGGTPPRVCVQQGGSSELNLAQFYREHGVAYRPVAFGSLE 191 Query: 179 EGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDI 238 E + + AG CD ++ D L R+ L D V+ P +ISK PLGP+VR GD+ W ++ Sbjct: 192 EAARAYDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISKSPLGPIVRQGDDQWFNV 251 Query: 239 VRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILA 298 VRW+ +A+V AEE G+ A + A S+ P++RRL+G +GD G+ +GL D+A R I Sbjct: 252 VRWTLFAMVDAEELGV-DAKTVDAALSSDIPDLRRLVGSDGDFGEGLGLRPDWAYRVIHE 310 Query: 299 SGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 GNY EVF+ N+G S+ + R NA W++GGLMYAPP R Sbjct: 311 VGNYAEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350 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: 297 Number of extensions: 12 Number of successful extensions: 3 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: 350 Length adjustment: 29 Effective length of query: 309 Effective length of database: 321 Effective search space: 99189 Effective search space used: 99189 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 09 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