Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF966 PS417_04900 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__WCS417:GFF966 Length = 343 Score = 342 bits (877), Expect = 8e-99 Identities = 175/340 (51%), Positives = 227/340 (66%), Gaps = 2/340 (0%) Query: 1 MKKSVFFGSVALAALVAGAASA-STLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDV 59 +K ++ S A V+G A A +TLD V+ +G + CG + GL GF+ PDA+G G D Sbjct: 4 LKSTLAIVSAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDASGKILGIDA 63 Query: 60 AVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVA- 118 VC+AVAAAV GD KVK+ L + RFTAL SGEVD+L RN+T T SRD + L F Sbjct: 64 DVCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEVDILSRNTTMTSSRDAGMGLKFPGF 123 Query: 119 VNYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDA 178 + YYDG GF+VN LGV SAKELDGATIC+Q GTTTE+N++D+F+ NN+ YTP+ Sbjct: 124 ITYYDGIGFLVNNKLGVKSAKELDGATICIQAGTTTELNVSDYFRGNNLKYTPITFDTSD 183 Query: 179 EGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDI 238 E + +G CD T+D S L + R+ L D V+LPE ISKEPLGPVVR+GD+ W I Sbjct: 184 ESAKSLESGRCDVLTSDKSQLFAQRSKLAAPKDYVVLPETISKEPLGPVVRNGDDEWLAI 243 Query: 239 VRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILA 298 VRW YA++ AEE GIT N+E A ST+NP++ RLLG +G+ GK + + D+ + + Sbjct: 244 VRWVGYAMLNAEEAGITSKNVEAEAKSTKNPDVARLLGADGEYGKDLKVKKDWVVQIVKQ 303 Query: 299 SGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 GNYGEVFE N+G ST + + RGLNA W GG+ YAPP R Sbjct: 304 VGNYGEVFERNLGKSTPLEIDRGLNALWNNGGIQYAPPVR 343 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: 328 Number of extensions: 12 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: 338 Length of database: 343 Length adjustment: 28 Effective length of query: 310 Effective length of database: 315 Effective search space: 97650 Effective search space used: 97650 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