Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate PP_3727 PP_3727 Amino-acid permease RocE
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Putida:PP_3727 Length = 468 Score = 249 bits (636), Expect = 2e-70 Identities = 151/482 (31%), Positives = 243/482 (50%), Gaps = 23/482 (4%) Query: 25 TGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLC 84 T V+ L + LK+RH+ M+++GG IG GLF+GSG + +GGP ++ YL+ G+++ Sbjct: 2 TDSVEKIQLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYL 61 Query: 85 TCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFW 144 + L E++V PV+G+F + +++ P+ GF +GW Y ++W T + E AA + + W Sbjct: 62 VMVCLGELSVQMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRW 121 Query: 145 REDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVG- 203 ++ + W ++F+VVL G+ R +GE E+ S IK+ +GFI++G+++ G + Sbjct: 122 FPEVPIWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPL 181 Query: 204 DQGYIGVKYWRDPGAFTSFKGFCAVFVV---AAFSFGGTEMVGLAAAESANPRKSIPMAS 260 G G G AVF V ++F G E++G+AA E+ +P KSIP A Sbjct: 182 SSGAPAPMLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAV 241 Query: 261 KQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNA 320 + V +R+ IFY+L + ++ I+P LM SPFV GI +MN Sbjct: 242 RNVVFRVLIFYVLAIAVLSAIVPHEQAGLM--------ESPFVQVFDMVGIPYAADLMNF 293 Query: 321 VITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIG 380 VI A+LSV NS + STR + AM++ MAP + +G PL + + + F L++ + Sbjct: 294 VILTAILSVGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLMT 353 Query: 381 AAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSY 440 + +F L+A++G+ W I LA R R G L + YK P Y Sbjct: 354 SFVAADTLFMVLMAVSGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKYKAPL-----Y 408 Query: 441 LGLGLNILALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYKACTRKRQMYVR 500 + L + L +S + L P S Y F + L Y Y R+RQ Sbjct: 409 PLVPLLCITLCSSLFVFLALDETQRP------SLYWGFGFIALCYAAYFFVNRRRQGAFA 462 Query: 501 PA 502 P+ Sbjct: 463 PS 464 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: 630 Number of extensions: 33 Number of successful extensions: 3 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: 468 Length adjustment: 34 Effective length of query: 502 Effective length of database: 434 Effective search space: 217868 Effective search space used: 217868 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