Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate 201983 SO2857 sodium/solute symporter family protein (NCBI ptt file)
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__MR1:201983 Length = 578 Score = 1001 bits (2589), Expect = 0.0 Identities = 496/578 (85%), Positives = 539/578 (93%), Gaps = 6/578 (1%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 M VQ LTYLIVG +FALYIGIA+W+RAGSTKEFYVAGGGVHPV+NGMATAADWMSAASFI Sbjct: 1 MGVQGLTYLIVGLSFALYIGIALWTRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFI 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDF+G+RYYSQAARTVA Sbjct: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFLGERYYSQAARTVA 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 V+CAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFY+VLGGMKGITYTQVA Sbjct: 121 VICAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYSVLGGMKGITYTQVA 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240 QYCVLIFAFMVPAIF+SVMMTGHI+PQ+GFGA+L+DAAGNN+GVYLL+KL+ LS LGF+ Sbjct: 181 QYCVLIFAFMVPAIFLSVMMTGHIIPQIGFGAQLLDAAGNNSGVYLLDKLNNLSVDLGFA 240 Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300 YT+GSK MIDV ITGALM GTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT+ Sbjct: 241 PYTDGSKSMIDVLCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTV 300 Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGE-- 358 PALAAFSRVNMIETINGP+ GVAYETAP+WIKNWEKTGLIKWDDKN DGKIYYA G+ Sbjct: 301 PALAAFSRVNMIETINGPDQKGVAYETAPNWIKNWEKTGLIKWDDKNGDGKIYYATGKIE 360 Query: 359 ----TNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL 414 TNEMKID DI+VLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL Sbjct: 361 DAASTNEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL 420 Query: 415 LKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAII 474 LKKN MP+ISDK+EL+YAR+AA +GIV+AGYFG+NPPGFVAAVVA AFGLAASSLFPAII Sbjct: 421 LKKNLMPNISDKKELMYARLAAGIGIVIAGYFGVNPPGFVAAVVAFAFGLAASSLFPAII 480 Query: 475 MGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWLFGISPEGIGMLGMII 534 MGIFS+TMNKEGAIAGM++GL F++ YI+YFKF++P N +NW GISPEGIGM+GM+I Sbjct: 481 MGIFSKTMNKEGAIAGMILGLFFTSGYIVYFKFIDPTANVPANWFLGISPEGIGMVGMVI 540 Query: 535 NFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572 NF VA IVSKVTAA P +V +MVESIRFPKGAGEA DH Sbjct: 541 NFVVAAIVSKVTAATPVHVQEMVESIRFPKGAGEASDH 578 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: 1311 Number of extensions: 43 Number of successful extensions: 2 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: 572 Length of database: 578 Length adjustment: 36 Effective length of query: 536 Effective length of database: 542 Effective search space: 290512 Effective search space used: 290512 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