Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate PfGW456L13_2421 Acetate permease ActP (cation/acetate symporter)
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421 Length = 548 Score = 162 bits (409), Expect = 4e-44 Identities = 139/496 (28%), Positives = 220/496 (44%), Gaps = 80/496 (16%) Query: 15 FALY-IGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGY 71 F L+ +G+ W+ R ST +FY AGGG+ NG+A A D +SAASF+ ++ ++ GY Sbjct: 40 FVLFTLGVTRWAALRTRSTSDFYTAGGGMTGFQNGLAIAGDMISAASFLGISAMMFLNGY 99 Query: 72 DGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFICFTY 131 DG +Y +G G+ ++ +A LR GK+T D + R R + + + Y Sbjct: 100 DGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLEQTPVRLTSAFGTLTVALMY 159 Query: 132 IAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIFAFMV 191 + QM G G + ++ V + ++ FY GGM T+ Q+ + +L+F Sbjct: 160 LVAQMVGAGKLIELLFGIDYLYAVMLVGVLMVFYVTFGGMLATTWVQIIKAVMLLFGTSF 219 Query: 192 PAIFISVMMTGHILPQLGFGAELVDAAGN---NTGVYLLEKLDGLSAQLGFSQYTEGSKG 248 A F+ + G + GA V A GN G L +D +S LG Sbjct: 220 MA-FMVLKHFGFSTEAMFAGATAVHAKGNAIMAPGGLLSNPIDAISLGLG---------- 268 Query: 249 MIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSR 308 +MFGTAGLPH+++RFFTV K+AR S +A FI Y + + F Sbjct: 269 ----------MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLL-IIVGFGA 317 Query: 309 VNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETNEMKIDRDI 368 + M+ T A+ A G I G N + + Sbjct: 318 IVMV-------GTDPAFRDA--------------------SGAII---GGGNMVAVH--- 344 Query: 369 MVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL----LKKNFMPDIS 424 LA NL + ++A A L+ AGL L +++VSHDL ++K S Sbjct: 345 --LAHAVGGNL---FLGFISAVAFATILAVVAGLALSGASAVSHDLYACVMRKG---QAS 396 Query: 425 DKQELLYARIA----AALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSR 480 ++QE+ +RIA L IV+ F F++ +V +AAS FP + + ++ + Sbjct: 397 EQQEMRVSRIATLCIGVLAIVLGLLFESQNIAFLSGLV---LAIAASVNFPVLFLSMYWK 453 Query: 481 TMNKEGAIAGMVIGLL 496 + GA+ G + GL+ Sbjct: 454 GLTTRGAVLGSLSGLV 469 Lambda K H 0.326 0.140 0.423 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: 899 Number of extensions: 54 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 572 Length of database: 548 Length adjustment: 36 Effective length of query: 536 Effective length of database: 512 Effective search space: 274432 Effective search space used: 274432 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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