Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate BWI76_RS13515 BWI76_RS13515 amino acid permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Koxy:BWI76_RS13515 Length = 485 Score = 892 bits (2306), Expect = 0.0 Identities = 439/480 (91%), Positives = 462/480 (96%) Query: 1 MKTQTTHAAEQHAAKRRWLNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAG 60 M T+ + AEQHAAKR WLN+ E GYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAG Sbjct: 1 MNTKHSSVAEQHAAKRHWLNSQESGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAG 60 Query: 61 PALALVYLICGIFSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAM 120 PALALVYL+CG+FSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYF+NWAM Sbjct: 61 PALALVYLVCGLFSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFVNWAM 120 Query: 121 TGIVDITAVALYMHYWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLA 180 TGIVDITAVALYMHYWGAFGDVPQWVFALGAL IVGTMNMIGVKWFAEMEFWFAL+KVLA Sbjct: 121 TGIVDITAVALYMHYWGAFGDVPQWVFALGALAIVGTMNMIGVKWFAEMEFWFALVKVLA 180 Query: 181 IVIFLVVGTIFLGTGQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVG 240 IV FLVVGTIFLG+G+PL+GNATGFHLITDNGG FPHGLLPALVL+QGVVFAFASIELVG Sbjct: 181 IVAFLVVGTIFLGSGKPLDGNATGFHLITDNGGLFPHGLLPALVLVQGVVFAFASIELVG 240 Query: 241 TAAGECKDPQKMVPKAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGV 300 TAAGECKDPQ MVP+AINSVIWRIGLFYVGSV+LLVLLLPWNAYQAGQSPFVTFFSKLGV Sbjct: 241 TAAGECKDPQTMVPRAINSVIWRIGLFYVGSVLLLVLLLPWNAYQAGQSPFVTFFSKLGV 300 Query: 301 PYIGSIMNIVVLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATL 360 PYIGS+MNIVVLTAALSSLNSGLYCTGRILRSMSMGGSAPKFM+KMSR HVPYAGILATL Sbjct: 301 PYIGSVMNIVVLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMSKMSRHHVPYAGILATL 360 Query: 361 VVYVVGVFLNYLVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLP 420 VYVVGVFLNYLVPS+VFEIVLN ASLGIIASW FI+VCQMRLR+AIKEGKAADVSFK+P Sbjct: 361 GVYVVGVFLNYLVPSQVFEIVLNVASLGIIASWGFIVVCQMRLRKAIKEGKAADVSFKMP 420 Query: 421 GAPFTSWLTLLFLLSVLVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVAEIHRTAP 480 GAPFTSWLTLLFLLSVLVLMAFDYPNGTYTI S+PLIA+LLVAGWFGVR+RV +IH TAP Sbjct: 421 GAPFTSWLTLLFLLSVLVLMAFDYPNGTYTIGSIPLIAVLLVAGWFGVRKRVHDIHSTAP 480 Lambda K H 0.328 0.140 0.434 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: 966 Number of extensions: 48 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: 497 Length of database: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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