Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 284 bits (726), Expect = 6e-81 Identities = 154/473 (32%), Positives = 251/473 (53%), Gaps = 11/473 (2%) Query: 28 VKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCL 87 V++ L++ LK RH+ MIAIGGA+G GLFV SG ++ + GP L+ Y +IG+M+ C Sbjct: 13 VEHDDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMT 72 Query: 88 ALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWRED 147 +L E+AV PV G+F TY +V+ +GFA+GW Y + + EL AA + +++W Sbjct: 73 SLGELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPH 132 Query: 148 INMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG---GVGD 204 ++ VW + FL+++ G+ F VRG+GE E+ ++IK+ + F+ G+++ G G Sbjct: 133 VSGVVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQ 192 Query: 205 QGYIGVKYWRDP--GAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQ 262 G+ P G + G V ++A FSF GTE VG+AA E+A+P ++IP A +Q Sbjct: 193 SGWHNFTLGDAPFVGGIPAMFG---VAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQ 249 Query: 263 VFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVI 322 FWRI +FY+L + I+G+++P DP L+ + SPF L + AG+ +MNAV+ Sbjct: 250 TFWRILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVV 309 Query: 323 TVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAA 382 A+LS S + STR + +A AP + + G P + A G L ++ + Sbjct: 310 LTALLSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSL 369 Query: 383 PQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLG 442 ++ WLL +G+ W I ++H R R G+ QG + Y++P G Sbjct: 370 FGDKAVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFA 429 Query: 443 LGLNILALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYKACTRKR 495 + L ++ ++ Y A G +Y+ +L+LGY+ + R Sbjct: 430 IVLCVVIVLGQNYQAFSDVRG---RWLEIVGTYIGVPLFLVLWLGYRLVKKTR 479 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: 667 Number of extensions: 34 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: 536 Length of database: 509 Length adjustment: 35 Effective length of query: 501 Effective length of database: 474 Effective search space: 237474 Effective search space used: 237474 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