Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate RR42_RS13875 RR42_RS13875 sodium:solute symporter
Query= reanno::PV4:5209923 (572 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS13875 RR42_RS13875 sodium:solute symporter Length = 683 Score = 194 bits (492), Expect = 1e-53 Identities = 100/219 (45%), Positives = 136/219 (62%), Gaps = 6/219 (2%) Query: 2 DVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFIS 61 D L Y+ + T A+Y I + R E+YVAG V + NGMA AADWMSAASFI Sbjct: 39 DALWLGYVFLFVTIAIYACIGLICRTSDLNEYYVAGRRVPALFNGMAIAADWMSAASFIG 98 Query: 62 LAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRY------YSQA 115 LAGI+ GY+G Y+MGWTGGY L+A +APYLRK+G +T+PDF+ RY + Sbjct: 99 LAGILFASGYEGLAYVMGWTGGYCLVAFLLAPYLRKYGGYTIPDFLAARYGNGKPGGNMP 158 Query: 116 ARTVAVVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGIT 175 R +AV+ A F Y+ Q++GVG++ +RF+ VE GV+ G+A + + LGGM+ +T Sbjct: 159 VRAIAVMAASLCSFVYLVAQIQGVGLIVTRFIGVEFAVGVFFGLAGILVCSFLGGMRAVT 218 Query: 176 YTQVAQYCVLIFAFMVPAIFISVMMTGHILPQLGFGAEL 214 +TQVAQY +LI AF+V I+ LPQL +G L Sbjct: 219 WTQVAQYIMLIAAFLVTVSMIAWKHHHEALPQLSYGTLL 257 Score = 184 bits (467), Expect = 1e-50 Identities = 113/291 (38%), Positives = 156/291 (53%), Gaps = 13/291 (4%) Query: 259 LMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETINGP 318 LM GTA LPH++ R +T P VK++R S WA+ FIA++Y + PALAA + + + Sbjct: 386 LMLGTASLPHILTRLYTTPSVKESRNSVAWAVFFIALLYVSAPALAALVKYEFFQHL--- 442 Query: 319 ESTGVAYETAPDWIKNWEKTG--LIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATPEI 376 G Y P W+ W K + D N DG + +A E+ I D++VLA PEI Sbjct: 443 --VGTPYAELPQWVVQWRKVDPPVFGIRDVNGDGIVQWA-----EILIQPDMIVLAAPEI 495 Query: 377 ANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAA 436 A LP + LVAAG LAAALST+ GLLL I+ ++SHD+ S ++ + A+I Sbjct: 496 AGLPYVISGLVAAGALAAALSTADGLLLTIANALSHDVFYHMGDRTASHQRRVTTAKIVL 555 Query: 437 ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLL 496 + A Y PG + +V AF LAASS FP +++ IF R GA+AGMV GL Sbjct: 556 LGVALFASYVTSLRPGNILFLVGAAFSLAASSFFPVLVLAIFWRRTTAAGAVAGMVAGLG 615 Query: 497 FSASYI-IYFKFVNPGDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVT 546 + YI + + F N FG+ P G G+ FAVA +VS +T Sbjct: 616 VAVYYIFVNYPFFTRMTGIFGNRWFGVDPIASGAFGVPAGFAVAILVSLLT 666 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: 1058 Number of extensions: 67 Number of successful extensions: 8 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: 683 Length adjustment: 37 Effective length of query: 535 Effective length of database: 646 Effective search space: 345610 Effective search space used: 345610 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: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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