Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_011385006.1 AMB_RS13215 cation acetate symporter
Query= reanno::PV4:5209923 (572 letters) >NCBI__GCF_000009985.1:WP_011385006.1 Length = 554 Score = 160 bits (405), Expect = 1e-43 Identities = 143/557 (25%), Positives = 246/557 (44%), Gaps = 85/557 (15%) Query: 6 LTYLIVGFTFAL-YIGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISL 62 +T + + F F + +GI W+ R S +FY AGGG+ NG+A A D+MSAA+ + L Sbjct: 34 VTAIAMFFAFVMGTLGITYWASKRTKSASDFYTAGGGITGFQNGLAIAGDYMSAATLLGL 93 Query: 63 AGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVV 122 + +V G+DG +Y + + G+ ++ +A LR G++T D R RT A + Sbjct: 94 SSMVFATGFDGFIYTISFFVGWPIILFLLAERLRNLGRYTFADIASYRLDQSKVRTFAAM 153 Query: 123 CAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQY 182 ++ + Y+ QM G G + ++ V I ++ Y GGM T+ Q+ + Sbjct: 154 GSLTVVCFYLIVQMVGAGQLIKLLFGLDYAVAVIIVGVLMVVYVTFGGMIATTWVQIIKA 213 Query: 183 CVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNT----------GVYLLEKLDG 232 C+L+ V++ L + GF E V A + G L + + Sbjct: 214 CLLLGG--------GVLLCALALSKFGFSLENVAAKAVESHKAGVKIMGPGTMLADPVSA 265 Query: 233 LSAQLGFSQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVF 292 +S LG L+FGTA LPH+++RFFTVP K+AR S A F Sbjct: 266 VSLSLG--------------------LVFGTAALPHILMRFFTVPNAKEARKSVFVASGF 305 Query: 293 IAIMY--TTIPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDG 350 I + I LAA S V T P + + + G K N Sbjct: 306 IGFFFLIVCILGLAAVSIVG----------------TDPQFFEGGKVGG--KLLGGGNMP 347 Query: 351 KIYYAKGETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSV 410 ++ AK + DI + ++A A L+ +GL L ++++ Sbjct: 348 VMHLAKA------LGGDIF--------------LGFLSAVAFATILAVVSGLALAGASAI 387 Query: 411 SHDLLKKNFMP-DISDKQELLYARIAAALGIVMAGYFGIN-PPGFVAAVVAIAFGLAASS 468 +HD+ + ++ +E+ +++++ + V+A GI VA +V + FG+AAS+ Sbjct: 388 AHDIYARVIRKGHATEAEEMRVSKLSSLVLGVVAVILGIMFEKQNVAFLVGLTFGIAASA 447 Query: 469 LFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWLFGISPEGIG 528 FP + + ++ R + +GA+ G + GL+ + + ++ K V N +F E Sbjct: 448 NFPVLFLSMYWRGLTTKGALWGGIAGLVSAVTCVVLSKAVWVVVLNNPAPIFPY--EHPA 505 Query: 529 MLGMIINFAVAFIVSKV 545 + M + F V +VSK+ Sbjct: 506 LFSMTLAFLVTIVVSKL 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: 841 Number of extensions: 65 Number of successful extensions: 5 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: 554 Length adjustment: 36 Effective length of query: 536 Effective length of database: 518 Effective search space: 277648 Effective search space used: 277648 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