Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate Dsui_2006 Dsui_2006 putative sodium:solute symporter, VC_2705 subfamily
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__PS:Dsui_2006 Length = 680 Score = 214 bits (544), Expect = 1e-59 Identities = 123/331 (37%), Positives = 189/331 (57%), Gaps = 26/331 (7%) Query: 244 EGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPAL 303 E S ++ + LM GTA LPHV++R++T P VK+AR S W+L FI ++Y T PA Sbjct: 364 ESSAARLNFLTLMFCLMVGTAALPHVLMRYYTTPTVKEARESVTWSLFFILLLYFTAPAY 423 Query: 304 AAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETNEMK 363 A F++ + T+ +T +A+ P W+ W K GL+ +D N+DG + A E+ Sbjct: 424 AVFAKYEVYSTLI---NTPIAH--LPSWVAAWGKVGLVAIEDINHDGLLQLA-----ELS 473 Query: 364 IDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDI 423 ++ D++VLATPEIA LP + LVAAGGLAAALST+ GLLL I+ S+SHD+ K P Sbjct: 474 LNPDVIVLATPEIAGLPYVISGLVAAGGLAAALSTADGLLLTIAGSLSHDVYYKIIQPRA 533 Query: 424 SDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMN 483 S + L+ ++ + V+A P + +VA AF +AA++ FPA+++GIF + N Sbjct: 534 STQWRLVISKSLLLVTAVLAATVAAQRPATILYMVAWAFSIAAAAFFPALVIGIFWKRAN 593 Query: 484 KEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWL----------FGISPEGIGMLGMI 533 + GA++GMV+GLL + Y++ +F ++ WL FGI G+ G+ Sbjct: 594 RAGAVSGMVVGLLITVYYMVRVQF------DSVPWLGLRGIGMEPWFGIQSTSAGVWGVP 647 Query: 534 INFAVAFIVSKVTAAVPQNVVDMVESIRFPK 564 F +VS +T + V D VE + +P+ Sbjct: 648 AGFLTIVVVSLLTKPPSREVQDFVEQVHYPQ 678 Score = 212 bits (540), Expect = 3e-59 Identities = 100/207 (48%), Positives = 137/207 (66%) Query: 8 YLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVS 67 Y + FT +Y I + SR E+YVAG V + NGMAT ADWMSAASFI +AG + Sbjct: 44 YAFLLFTILIYATIGVMSRTADVSEYYVAGRRVPALFNGMATGADWMSAASFIGMAGTLY 103 Query: 68 FVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFI 127 GY G Y+MGWTGGYVL+AL +APYLRKFG++T+PDF+ RY A R V V AI Sbjct: 104 LTGYQGLAYIMGWTGGYVLVALFLAPYLRKFGQYTIPDFLAVRYGGNAPRLVGVAAAIIA 163 Query: 128 CFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIF 187 F Y+ Q+ GVG++ SRF+ ++ + GV++G+A + + LGGM+ +T+TQVAQY +LI Sbjct: 164 SFVYVVAQIYGVGLITSRFVSLQFEIGVFVGLAGILVCSFLGGMRAVTWTQVAQYVILII 223 Query: 188 AFMVPAIFISVMMTGHILPQLGFGAEL 214 A++ P +S +T +PQL +G L Sbjct: 224 AYVTPVALLSFQITSVPVPQLVYGEVL 250 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: 1040 Number of extensions: 53 Number of successful extensions: 7 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: 680 Length adjustment: 37 Effective length of query: 535 Effective length of database: 643 Effective search space: 344005 Effective search space used: 344005 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