Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AZOBR_RS00530 AZOBR_RS00530 putative amino-acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__azobra:AZOBR_RS00530 Length = 349 Score = 270 bits (690), Expect = 4e-77 Identities = 147/340 (43%), Positives = 202/340 (59%), Gaps = 9/340 (2%) Query: 6 FFGSVALAALVAGAASA-------STLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFD 58 F + +AA++A A SA T++DV+ RG L CG + G AA D +G ++GF Sbjct: 7 FARAAVVAAVLAAAVSAPSGGPRAETMEDVRERGLLRCGVSSSGAGLAAVDDSGNWRGFF 66 Query: 59 VAVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVA 118 V +C+A+AAAV G +V++V E RF L +GEVDV++ +TWT RD +DF A Sbjct: 67 VDMCRALAAAVAGKADRVEFVETNSENRFAILRNGEVDVVMEGTTWTLQRDATFGIDFPA 126 Query: 119 VNYYDGQGFMVNKSLGVSSAKELD-GATICVQTGTTTEMNLADFFKANNMTYTPVNIADD 177 V +DGQGF+ +++ GV+ +L GA++CV TTT NL D+ + + + Sbjct: 127 VYLFDGQGFIAHRAHGVARLSDLPPGASVCVIEQTTTLRNLEDWMARTGVRFRLKRVRST 186 Query: 178 AEGQQKFAAGACDSYTTDASGLASSRAT-LPNAADIVILPEIISKEPLGPVVRHGDNNWG 236 F CD YT+D GL + R P D VILPE ISKEPLGP+VR + W Sbjct: 187 EGALSAFFNHHCDLYTSDRIGLHAQRLLKAPERDDYVILPEAISKEPLGPMVRPDERRWF 246 Query: 237 DIVRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAI 296 DIVRW F A V AEE GIT AN + Q+PE+RRLLG +G +GLD+D+A R I Sbjct: 247 DIVRWVFLATVLAEEKGITAANAPRLKEEAQDPEVRRLLGATTGVGWGLGLDDDWAFRVI 306 Query: 297 LASGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPP 336 GNYGE+F+ ++GA++ +G+ RG+N W GGL YAPP Sbjct: 307 TQVGNYGEIFDRHLGAASPLGIDRGMNGLWMNGGLHYAPP 346 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: 296 Number of extensions: 10 Number of successful extensions: 4 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: 349 Length adjustment: 29 Effective length of query: 309 Effective length of database: 320 Effective search space: 98880 Effective search space used: 98880 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