Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 208 bits (530), Expect = 3e-58 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 22/396 (5%) Query: 33 LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEM 92 L + LK+RH+QMIAIGGAIG GLF+G+G A+ GP L++ Y I G+ + AL E+ Sbjct: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPG-LMLSYAIGGVAIFFIMRALGEL 77 Query: 93 AVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAV 152 + PV+G+F TY FV P GFA GW Y W+ E+ A ++ + +W D+ + Sbjct: 78 LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137 Query: 153 WVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIG--V 210 L VL + V +GE+EF ++IK+ V I++G+ I GV G Sbjct: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFS 197 Query: 211 KYWRDPGAFTSF--KGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIA 268 W G F F G + F++ G E++G+ A E+ NP K +P A+ V WRI Sbjct: 198 NLWTH-GGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRIL 256 Query: 269 IFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLS 328 IFY+ L I+ ++P N+ SPFV + G+ +I+N V+ A S Sbjct: 257 IFYVGALIIMMALVPWNE--------LKPGVSPFVYVFERIGVPGAAAIVNLVVITAAAS 308 Query: 329 VANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAF----GLLAYIGAAPQ 384 NS F + R + +A+ AP F + SK P + A LL YI P+ Sbjct: 309 SCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYI--VPE 366 Query: 385 GMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKA 420 ++F W+ +++ +G L+ W I +AH+ R + A Sbjct: 367 --QVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAA 400 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: 623 Number of extensions: 37 Number of successful extensions: 5 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: 472 Length adjustment: 34 Effective length of query: 502 Effective length of database: 438 Effective search space: 219876 Effective search space used: 219876 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