Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_012405807.1 BPHY_RS32965 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_000020045.1:WP_012405807.1 Length = 484 Score = 195 bits (496), Expect = 3e-54 Identities = 143/441 (32%), Positives = 214/441 (48%), Gaps = 37/441 (8%) Query: 37 LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96 L+ RH+ MI++GG IGAGLFVGS L GP A + YL+ GI++L L EMA+ Sbjct: 26 LRQRHVTMISLGGIIGAGLFVGSSATLSTVGPGAC-VSYLVAGIVVLLVMRMLGEMALAV 84 Query: 97 PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVS- 155 P G+F Y + GF GW Y W+ V+ E +A + ++ W + VW+ Sbjct: 85 PGIGSFTEYARIGLGDWAGFTSGWLYWYFWVIVVAVEAVAGAAILQRWTP---VPVWMIG 141 Query: 156 -VFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVKYWR 214 V L V+ I + V+ YGE EF + IK+ A + FI++G G G W Sbjct: 142 LVLLSVMTLINLMSVKSYGEFEFWFASIKVAAIIVFIVIGAAWVFGLGHTHGA-----WI 196 Query: 215 DPGAFTSFKGFCAVFVVAA-----FSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269 + A F F + V AA F+ GG E+ +AAAES NP KS+ ++ V R+ Sbjct: 197 NLTAAKGFLPFGTMSVFAAVPTVIFAVGGAEIATIAAAESDNPAKSVAAMTRSVILRVIT 256 Query: 270 FYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSV 329 FY+ ++F++ I+P T SPFV A++ + IMNA++ VAVLS Sbjct: 257 FYVGSMFLIACIVPWTT--------IVTGHSPFVAALETMRVPGSADIMNAIVLVAVLSA 308 Query: 330 ANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIF 389 NS + S+R + +A R AP + P V+L G +A I A +F Sbjct: 309 LNSGLYVSSRILFRLAGRGDAPRALLRLTPSRVPRLAVLLSSVVGYIAIIAAIVSPQGVF 368 Query: 390 GWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGL-------IPYKTPFGVAGSYLG 442 +L+ +G LFV+ + LA IR+R + A+G+ L + Y + G L Sbjct: 369 LFLVNASGAVMLFVYLATALAQIRIRRRLAAKGVQPELPMWLFPWLSYAVVAAIVGVLLA 428 Query: 443 LGLN------ILALIASFYTA 457 +G++ ++A IAS A Sbjct: 429 MGMDAELRPQLMASIASLAVA 449 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: 607 Number of extensions: 36 Number of successful extensions: 6 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: 484 Length adjustment: 34 Effective length of query: 502 Effective length of database: 450 Effective search space: 225900 Effective search space used: 225900 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 Apr 09 2024. 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