Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PP_1297 PP_1297 putative amino-acid ABC transporter-binding protein YhdW
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__Putida:PP_1297 Length = 342 Score = 355 bits (912), Expect = e-103 Identities = 177/335 (52%), Positives = 227/335 (67%), Gaps = 1/335 (0%) Query: 4 SVFFGSVALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCK 63 +V + AL A V+ A + +TLD VK +G + CG + GL GF+ PDA G G D VC+ Sbjct: 9 AVLTAAAALGA-VSTAQAGATLDAVKKKGFVQCGVSDGLPGFSVPDAQGKIVGIDADVCR 67 Query: 64 AVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYD 123 AVAAAV GD KVK+ L + RFTAL SGEVDVL RN+TWT SRD + L F V YYD Sbjct: 68 AVAAAVFGDATKVKFSQLNAKERFTALQSGEVDVLSRNTTWTSSRDAGMGLVFAGVTYYD 127 Query: 124 GQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQK 183 G GF+VNK LGVSSAKELDGATIC+Q GTTTE+N++DFF+AN + YTP+ E + Sbjct: 128 GVGFLVNKKLGVSSAKELDGATICIQAGTTTELNVSDFFRANGLKYTPITFDTSDESAKS 187 Query: 184 FAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSF 243 +G CD T+D S L + R+ L + V+LPE ISKEPLGPVVR GD W IV+W+ Sbjct: 188 LESGRCDVLTSDKSQLFAQRSKLAAPTEYVVLPETISKEPLGPVVRKGDEEWFSIVKWTL 247 Query: 244 YALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYG 303 +A++ AEE GIT N+E A +T+NP++ RLLG +G+ GK + L D+ + + GNYG Sbjct: 248 FAMLNAEEAGITSKNVEAEAKATKNPDVARLLGADGEYGKDLKLPKDWVVQIVKQVGNYG 307 Query: 304 EVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 EVFE N+G ST + + RG+NA W GG+ YAPP R Sbjct: 308 EVFEKNLGQSTDLKIDRGMNALWNNGGIQYAPPVR 342 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: 325 Number of extensions: 7 Number of successful extensions: 1 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: 342 Length adjustment: 28 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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