Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__azobra:AZOBR_RS19235 Length = 556 Score = 171 bits (433), Expect = 7e-47 Identities = 148/541 (27%), Positives = 236/541 (43%), Gaps = 87/541 (16%) Query: 19 IGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSFVGYDGSVY 76 +GI W+ R S +FY AGGG+ NG+A A D+MSAA+F+ L+G+V G+DG +Y Sbjct: 53 LGITYWASKRTRSASDFYTAGGGISGFQNGLAIAGDYMSAAAFLGLSGMVFAKGFDGVIY 112 Query: 77 LMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFICFTYIAGQM 136 +G+ G+ L+ +A LR G+FT D R R++A V ++ + Y+ QM Sbjct: 113 TIGFLVGWPLMLFLIAERLRNLGRFTFADVASYRLGQTPIRSLAAVGSLTVVCFYLIAQM 172 Query: 137 RGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIFAFMVPAIFI 196 G G + ++ V + ++ Y GGM T+ Q+ + +L+ V Sbjct: 173 VGAGKLIQLLFGLDYTYAVVMVGVLMILYVTFGGMLATTWVQIIKAVMLLGGCTV----- 227 Query: 197 SVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFSQYTEGSKGMIDVFFIT 256 + G L Q GF E + L + + +A + + I ++ Sbjct: 228 ---LVGLALAQFGFNPERL----------LQQAVAAHAANAAILRPSAAMADPIAAVSLS 274 Query: 257 GALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETIN 316 ALM G AGLPH+++RFFTVP K+AR S +A FI + + + V + Sbjct: 275 LALMCGPAGLPHILMRFFTVPDAKEARKSVVYATGFIGYFFILTVTIGFLAIVIV----- 329 Query: 317 GPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATPEI 376 T AY A I N I+ +K + Sbjct: 330 ---GTNPAYLDAAGKILG-----------GGNMAAIHLSKAIGGNL-------------- 361 Query: 377 ANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL----LKKNFMPDISDKQELLYA 432 + ++A A L+ AGL L +++VSHDL LKK + ++ E+ + Sbjct: 362 ------FLGFISAVAFATILAVVAGLTLAGASAVSHDLYARVLKKG---NATEASEMRVS 412 Query: 433 RIAA-ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGM 491 R+A ALG++ + +A +V +AFGLAAS FP +I+ IF + + GA G Sbjct: 413 RLATLALGVIAITLGLLFENQNIAFMVGLAFGLAASVNFPVLILSIFWKGLTTRGAFIGG 472 Query: 492 VIGLLFSASYII--------YFKFVNPGDNNASNWLFGISP-EGIGMLGMIINFAVAFIV 542 GL+ ++++ FKF P I P E + M+I FA ++ Sbjct: 473 FAGLVSCVAFVVLGPTVWVSVFKFPAP-----------IFPYEHPALFSMVIAFATTWLF 521 Query: 543 S 543 S Sbjct: 522 S 522 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: 860 Number of extensions: 58 Number of successful extensions: 4 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: 556 Length adjustment: 36 Effective length of query: 536 Effective length of database: 520 Effective search space: 278720 Effective search space used: 278720 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