Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate AO356_28340 AO356_28340 GABA permease
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28340 Length = 466 Score = 223 bits (569), Expect = 9e-63 Identities = 140/400 (35%), Positives = 212/400 (53%), Gaps = 13/400 (3%) Query: 30 NGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLAL 89 NG L Q K RH+ M++I G IGAGLFVGSG A+ GPA +L YL G++++ L Sbjct: 10 NGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVML-AYLFSGLLVVLVMRML 68 Query: 90 AEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDIN 149 EMAV P G+F TY + + GF +GW Y W+ V+P E +AA + W ++ Sbjct: 69 GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAVD 128 Query: 150 MAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIG 209 ++ SV +V+L +F V YGE EF ++ K+ A +GFI LG + G + ++ G Sbjct: 129 AWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREASG 188 Query: 210 V-KYWRDPGAFTSFKGFCAV---FVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFW 265 + + + G F G AV F+ FSF GTE V +AAAES NP ++I A++ V W Sbjct: 189 LSRLMEEHGGFAP-NGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIW 247 Query: 266 RIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVA 325 RI +FY+L++F+V ++P NDP L + A++ I +++ V+ +A Sbjct: 248 RIGVFYLLSIFVVISVVPWNDPLL-------ASVGSYQRALELMNIPHAKFLVDMVVLIA 300 Query: 326 VLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQG 385 V S NS + ++R + ++ R AP K S G P VI G + + Sbjct: 301 VASCMNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMP 360 Query: 386 MEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINL 425 +F +LLA +G L V+ I ++ +RMR M+ Q I L Sbjct: 361 AGLFQFLLASSGAIALLVYLVIAISQLRMRRMMQRQNIEL 400 Lambda K H 0.327 0.142 0.442 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: 559 Number of extensions: 27 Number of successful extensions: 5 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: 536 Length of database: 466 Length adjustment: 34 Effective length of query: 502 Effective length of database: 432 Effective search space: 216864 Effective search space used: 216864 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