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) >FitnessBrowser__Cup4G11:RR42_RS13875 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:
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