Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_082697561.1 AQZ52_RS05130 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_001519075.1:WP_082697561.1 Length = 469 Score = 159 bits (403), Expect = 2e-43 Identities = 127/424 (29%), Positives = 199/424 (46%), Gaps = 31/424 (7%) Query: 24 ETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLL 83 E G + L + L RH+ MIAIGG IGAGLFVGS + GPAA +I YLI G+++L Sbjct: 17 EAGGAGSVELSRTLLPRHVSMIAIGGIIGAGLFVGSSTTIALTGPAA-VISYLIAGLLIL 75 Query: 84 CTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRF 143 +AEMA++ F + + GF GW Y W+ V+ E IA + I Sbjct: 76 LVMRMIAEMAIVLEGVRTFPDFARAGLGHLAGFLSGWLYWYFWVVVVAVEAIAGAKIIGG 135 Query: 144 WREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVG 203 W + + ++ G+ + R YGE EF S IK+ A + F ++ + G Sbjct: 136 WLPGVPEWAIGAGLTALMTGVNLMSTRSYGEFEFWFSSIKVAAILVFSLICALWVFGITA 195 Query: 204 DQGYIGVKYWRDPGAFTSFKGFC--------AVFVVAAFSFGGTEMVGLAAAESANPRKS 255 QG+ G T+ GF A FS G E+ +AAAES +P K Sbjct: 196 PQGF-------SIGNLTAHGGFAPHGWGPVLAGVASTIFSLCGAEIATIAAAESPDPAKV 248 Query: 256 IPMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLP 315 I + V RI IFY+L + ++ ++P SPF + I Sbjct: 249 IARMTVSVALRIVIFYVLAIGLIVAVVPWTQ--------IVPGHSPFATTLAAMHIPGGE 300 Query: 316 SIMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGL 375 +IM+AV+ VAVLS NS + ++R + +A AP++ +++++G P + IA L Sbjct: 301 TIMSAVVLVAVLSCLNSGLYVTSRALFGLARFGDAPDWLVHVNARGVPARAI---IAASL 357 Query: 376 LAYIGAAPQGME---IFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQG-INLGLIPYK 431 AY A Q + +F +L+ +G+ + ++ + +A ++ R M+ + L L + Sbjct: 358 FAYGALAAQWLSPGTVFSFLVNSSGVTMILLYALVGIAQLKERTRMEREAPERLTLKMWF 417 Query: 432 TPFG 435 PFG Sbjct: 418 HPFG 421 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: 595 Number of extensions: 24 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: 469 Length adjustment: 34 Effective length of query: 502 Effective length of database: 435 Effective search space: 218370 Effective search space used: 218370 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 24 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