Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Pf1N1B4_917 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917 Length = 343 Score = 337 bits (863), Expect = 3e-97 Identities = 169/335 (50%), Positives = 222/335 (66%), Gaps = 5/335 (1%) Query: 9 SVALAALVAG----AASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKA 64 ++ AA V G A + +TLD V+ +G + CG + GL GF+ PD+ G G D C+A Sbjct: 9 AIVTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRA 68 Query: 65 VAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVA-VNYYD 123 VAAAV GD KVK+ L + RFTAL SGE+DVL RNST T SRD + L F + YYD Sbjct: 69 VAAAVFGDATKVKFSQLNAKERFTALQSGEIDVLSRNSTMTSSRDAGMGLKFPGFITYYD 128 Query: 124 GQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQK 183 G GF+ N LGV SAKELDGATIC+Q GTTTE+N++D+F+AN + YTP+ E + Sbjct: 129 GIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKS 188 Query: 184 FAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSF 243 +G CD T+D S L + R+ L + D V+LPE ISKEPLGPVVR+GD+ W IVRW+ Sbjct: 189 LESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTG 248 Query: 244 YALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYG 303 YAL+ AEE G+T N+E A ST+NP++ R+LG +G+ GK + L D+ + + GNYG Sbjct: 249 YALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVKIVKQVGNYG 308 Query: 304 EVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 E+FE N+G T + + RGLNA W GG+ YAPP R Sbjct: 309 EMFERNLGKDTPLQIDRGLNALWNAGGIQYAPPVR 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: 323 Number of extensions: 10 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 Apr 09 2024. 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