Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate HSERO_RS03215 HSERO_RS03215 sodium:solute symporter
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__HerbieS:HSERO_RS03215 Length = 683 Score = 206 bits (525), Expect = 2e-57 Identities = 118/311 (37%), Positives = 179/311 (57%), Gaps = 20/311 (6%) Query: 259 LMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETINGP 318 LM GTA LPH+++R++T P V AR S W L FI ++Y T+PAL + ++ ++ Sbjct: 387 LMLGTAALPHILMRYYTTPTVAGARTSVFWTLFFIMLIYLTVPALTVLVKYDIYTSL--- 443 Query: 319 ESTGVAYETAPDWIKNWEKTG----LIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATP 374 G +Y PDW+ W L+ D N DG + + E+ +D DI+VLA P Sbjct: 444 --VGSSYSHLPDWVYYWANMDKLNPLVSITDLNRDGLV-----QLGEISMDGDIIVLAMP 496 Query: 375 EIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARI 434 EIA LP +V LVAAGGLAAALST+ GLLL IS ++SHD+ K P S ++ + +++ Sbjct: 497 EIAGLPYFVSGLVAAGGLAAALSTADGLLLTISNALSHDVYYKVVDPSASTQKRVTISKL 556 Query: 435 AAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIG 494 + ++A Y PG + ++V AF LAAS+LFPA+++G+F + N+ GAIAG++ G Sbjct: 557 LLLVVALLAAYAASLKPGDILSMVGAAFSLAASTLFPALVLGVFWKRANQAGAIAGILCG 616 Query: 495 LLFSASYIIYFKFVNP--GDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQN 552 L Y+++ NP G + A W F I+P G+ G+ + A IVS +T + Sbjct: 617 FLMCVYYMLH---TNPSFGGSAAGQW-FHIAPISAGIFGVPVGMAAMVIVSLLTPPPDEA 672 Query: 553 VVDMVESIRFP 563 + +++ IR P Sbjct: 673 TIALIDHIRTP 683 Score = 203 bits (517), Expect = 2e-56 Identities = 98/214 (45%), Positives = 141/214 (65%), Gaps = 7/214 (3%) Query: 8 YLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVS 67 YL + T LY GI + R E+YVAG V P+ NGMATAADW+SAA+FISLAG + Sbjct: 44 YLFLFVTIGLYAGIGVVCRTSDVPEYYVAGRRVPPLFNGMATAADWISAATFISLAGGLY 103 Query: 68 FVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQ-------AARTVA 120 G+DG Y++GWTGGY L+AL +APYLRKFG++T+ DF+ RY + R +A Sbjct: 104 LQGFDGLAYILGWTGGYCLVALLIAPYLRKFGQYTIADFLAARYPGRPGSQGVNVIRILA 163 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 V I I FTY+ Q+ GVG++ SRF ++ G+++G+A + + LGGM+ IT+TQVA Sbjct: 164 VAATILISFTYVVAQIYGVGLITSRFTGIDFSIGIFLGLASILVCSFLGGMRAITWTQVA 223 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAEL 214 QY +++ A+++P I++S T +P + +GA L Sbjct: 224 QYIIILLAYLIPVIWLSAKHTTVPVPPVAYGAVL 257 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: 1034 Number of extensions: 53 Number of successful extensions: 6 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