Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AZOBR_RS08655 AZOBR_RS08655 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__azobra:AZOBR_RS08655 Length = 340 Score = 369 bits (948), Expect = e-107 Identities = 187/341 (54%), Positives = 232/341 (68%), Gaps = 4/341 (1%) Query: 1 MKKSVFFGSVALAAL--VAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFD 58 MK + + A V GA + TLD VK RG + CG N GL GF PD++G + G D Sbjct: 1 MKSGILAAAAAAVVFGAVTGAQAGPTLDAVKGRGFVQCGVNAGLPGFGNPDSSGNWTGLD 60 Query: 59 VAVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVA 118 V C+AVA A+ DP KVK+ PL+ + RF A+ SGEVD+L RN+T T +RDT + L+F Sbjct: 61 VDYCRAVAVALFNDPNKVKFTPLSAQQRFPAIQSGEVDLLSRNTTVTLTRDTSVGLNFAP 120 Query: 119 VNYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDA 178 V YYDGQGFMVNK LGV SAKEL+GAT+CVQ GTTTE+NLAD+F+ NNM+Y PV I + Sbjct: 121 VTYYDGQGFMVNKKLGVKSAKELNGATVCVQAGTTTELNLADYFRTNNMSYNPVVIESND 180 Query: 179 EGQQKFAAGACDSYTTDASGLASSRA-TLPNAADIVILPEIISKEPLGPVVRHGDNNWGD 237 E + AG CD TTDASGLA +RA P D +ILPEIISKEPL P VRHGD+ W D Sbjct: 181 EVNAAYFAGRCDVLTTDASGLAGTRAGVAPVPDDHIILPEIISKEPLAPAVRHGDDQWFD 240 Query: 238 IVRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIL 297 +V+W+ YA + AEE GIT N++E +++NPEI+R+LG MGK +GLD +A I Sbjct: 241 VVKWTVYATIQAEEMGITSKNVDEF-VNSKNPEIQRILGTSPGMGKALGLDEKWAYNIIK 299 Query: 298 ASGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 GNYGE+FE N+G T + L RGLNA WT GGL YA P R Sbjct: 300 TMGNYGEIFERNVGTKTPLKLERGLNALWTNGGLQYAMPIR 340 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: 364 Number of extensions: 15 Number of successful extensions: 3 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: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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