Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 188 bits (478), Expect = 3e-52 Identities = 131/393 (33%), Positives = 196/393 (49%), Gaps = 19/393 (4%) Query: 33 LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEM 92 LK+ LK RH+ MIA+GG IGAGLFVGSG + GPAA+L YLI G+M+ L EM Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAIL-SYLIGGVMVTLVMFMLGEM 64 Query: 93 AVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAV 152 A P +G+F TY ++ GFA+GW Y + + E I + + + + Sbjct: 65 ASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPA 124 Query: 153 WVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG---GVGDQGYIG 209 L+ LM + VR +GE E+ LS K+ + F++LG I G G+ G + Sbjct: 125 GALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAPGLLN 184 Query: 210 VKYWRDPGAFTSFKGFCAVF---VVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWR 266 + D G F G V +V FS GG+E+ +AA ES NP K++ A K V R Sbjct: 185 LT---DHGGFMP-NGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILR 240 Query: 267 IAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAV 326 + +FY+ ++ I+ L +P D AN K SP+V AG M V+ V+ Sbjct: 241 VMVFYVGSVSILILCMPWTDK-------ANLK-SPYVSLFSMAGFTGAAVAMKIVLFVSF 292 Query: 327 LSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGM 386 +SV NS F ++R + ++++R AP F ++KG P+ ++L + + G Sbjct: 293 MSVMNSFLFSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGG 352 Query: 387 EIFGWLLALTGLGFLFVWGSICLAHIRMRAGMK 419 ++F L +G + VW I +AH MR K Sbjct: 353 DLFLMLAKSSGAFVMIVWIFIIVAHFAMRRQTK 385 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: 537 Number of extensions: 24 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: 459 Length adjustment: 34 Effective length of query: 502 Effective length of database: 425 Effective search space: 213350 Effective search space used: 213350 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