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 WP_086509147.1 BZY95_RS06440 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52812 (341 letters) >NCBI__GCF_002151265.1:WP_086509147.1 Length = 342 Score = 437 bits (1124), Expect = e-127 Identities = 215/341 (63%), Positives = 258/341 (75%), Gaps = 4/341 (1%) Query: 2 KNKLLSAAIGAAVLAVG-ASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFD 60 KNK L AAVLA+G AS ASA TL + +G VQCGV+ GL GF+APD G W G D Sbjct: 5 KNKWLLVT-SAAVLALGTASLASANTLQNTIQRGAVQCGVSDGLPGFSAPDDQGEWQGLD 63 Query: 61 VDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRP 120 VD C+AVA+AVFGD V+Y NA ERFTALQSGE+DVLSRNTTWT RDT LG NF Sbjct: 64 VDVCRAVAAAVFGDADAVRYISLNAVERFTALQSGEVDVLSRNTTWTTTRDTTLGLNFTG 123 Query: 121 VTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLP 180 VT+YDG GFM+ + L V SAL+L GAAICVQSGTTTELN+ADYF+ N ++++P+VF+ Sbjct: 124 VTFYDGIGFMINRDLGVSSALDLDGAAICVQSGTTTELNVADYFRANGMEFDPIVFDTSE 183 Query: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDI 240 + Y+AGRCDV T+D S L +LR+ L +PD+ +ILPEIISKEPLGP VRQGDDQWF+I Sbjct: 184 QTVGGYEAGRCDVLTSDTSQLAALRIQLSDPDQSVILPEIISKEPLGPVVRQGDDQWFNI 243 Query: 241 VSWTAYALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIK 300 V W+ +A++NAEE GITQ NVDEM+NS +PDI R LG D G +GL +WA N+I Sbjct: 244 VKWSLFAMLNAEEMGITQENVDEMRNSDDPDIARLLGQ--DGNYGEGMGLDANWAYNIIS 301 Query: 301 GVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 VGNYGE FERN+G GSPL+I RG+NALW GGIQYAPP+R Sbjct: 302 QVGNYGESFERNVGMGSPLQIERGINALWTNGGIQYAPPIR 342 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: 425 Number of extensions: 17 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: 341 Length of database: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 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 24 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