Align AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate AZOBR_RS00530 AZOBR_RS00530 putative amino-acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__azobra:AZOBR_RS00530 Length = 349 Score = 290 bits (742), Expect = 4e-83 Identities = 155/341 (45%), Positives = 216/341 (63%), Gaps = 11/341 (3%) Query: 8 AAIGAAVLAVGASAAS----ATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDF 63 AA+ AAVLA SA S A T+ DV+ +G ++CGV++ G AA D SGNW GF VD Sbjct: 10 AAVVAAVLAAAVSAPSGGPRAETMEDVRERGLLRCGVSSSGAGLAAVDDSGNWRGFFVDM 69 Query: 64 CKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTY 123 C+A+A+AV G +V++ TN++ RF L++GE+DV+ TTWT+ RD G +F V Sbjct: 70 CRALAAAVAGKADRVEFVETNSENRFAILRNGEVDVVMEGTTWTLQRDATFGIDFPAVYL 129 Query: 124 YDGQGFMVRKGLNVKSALEL-SGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEV 182 +DGQGF+ + V +L GA++CV TTT NL D+ +++ + Sbjct: 130 FDGQGFIAHRAHGVARLSDLPPGASVCVIEQTTTLRNLEDWMARTGVRFRLKRVRSTEGA 189 Query: 183 NAAYDAGRCDVYTTDQSGLYSLRLTLKNP--DEHIILPEIISKEPLGPAVRQGDDQWFDI 240 +A+ CD+YT+D+ GL++ RL LK P D+++ILPE ISKEPLGP VR + +WFDI Sbjct: 190 LSAFFNHHCDLYTSDRIGLHAQRL-LKAPERDDYVILPEAISKEPLGPMVRPDERRWFDI 248 Query: 241 VSWTAYALINAEEFGITQANVDEMK-NSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVI 299 V W A + AEE GIT AN +K + +P+++R LG+ T +G LGL +DWA VI Sbjct: 249 VRWVFLATVLAEEKGITAANAPRLKEEAQDPEVRRLLGATTG--VGWGLGLDDDWAFRVI 306 Query: 300 KGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPV 340 VGNYGEIF+R++G SPL I RG+N LW GG+ YAPP+ Sbjct: 307 TQVGNYGEIFDRHLGAASPLGIDRGMNGLWMNGGLHYAPPL 347 Lambda K H 0.316 0.134 0.398 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: 295 Number of extensions: 13 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: 341 Length of database: 349 Length adjustment: 29 Effective length of query: 312 Effective length of database: 320 Effective search space: 99840 Effective search space used: 99840 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