Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 228 bits (581), Expect = 4e-64 Identities = 139/402 (34%), Positives = 210/402 (52%), Gaps = 10/402 (2%) Query: 23 VETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIML 82 + + + + GL+Q LK RH+ M++I G IGAGLFVGSG A+ GPA LL Y G ++ Sbjct: 1 MSSSQSSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLL-AYAAAGALV 59 Query: 83 LCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIR 142 + L EMAV P G+F TY R + GF +GW Y W+ V+P E AA+ + Sbjct: 60 VLVMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILH 119 Query: 143 FWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGV 202 W ++ + + V ++L +F V+ YGE EF +++K+ A +GFI LGI+ G + Sbjct: 120 AWFPNVAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFL 179 Query: 203 GDQGYIGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMAS 260 GV + D F + FSF GTE+V +AAAES NP + I A+ Sbjct: 180 PTSQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKAT 239 Query: 261 KQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNA 320 V WRI +FY++++FIV ++P NDP L T ++ GI I++ Sbjct: 240 NSVIWRIGLFYLVSIFIVVALVPWNDPILASVGSYQT-------VLERMGIPNAKLIVDI 292 Query: 321 VITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIG 380 V+ VAV S NS + ++R + ++ +R AP + +S G P + V+L A LA Sbjct: 293 VVLVAVTSCLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFA 352 Query: 381 AAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQG 422 +F +LLA +G L V+ I ++ +RMR A+G Sbjct: 353 NYVAPAAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG 394 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: 574 Number of extensions: 28 Number of successful extensions: 4 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: 464 Length adjustment: 34 Effective length of query: 502 Effective length of database: 430 Effective search space: 215860 Effective search space used: 215860 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