Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate BPHYT_RS07010 BPHYT_RS07010 sodium:solute symporter
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__BFirm:BPHYT_RS07010 Length = 672 Score = 196 bits (498), Expect = 2e-54 Identities = 97/230 (42%), Positives = 142/230 (61%), Gaps = 13/230 (5%) Query: 8 YLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVS 67 Y+ + A+Y I + SR E+YVAG V NGMATAADW+SAASFI LAG + Sbjct: 40 YVFLFVPIAVYAVIGLLSRTSDLVEYYVAGRRVPSAFNGMATAADWLSAASFIGLAGSIY 99 Query: 68 FVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFI 127 GYDG YLMGWTGGY L+A +APY+RK ++T+PDF+G R+ S A R +A + A+ Sbjct: 100 ATGYDGLAYLMGWTGGYCLVAFLLAPYVRKLARYTIPDFLGTRFSSNAVRGLAALAAVLC 159 Query: 128 CFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLIF 187 F Y+ Q++GVG++ +RF+ V+ G++ G+A + + LGGM+ +T+TQVAQY +LI Sbjct: 160 SFVYLVAQIQGVGLIATRFIGVDFAVGIFCGLAGILVCSFLGGMRAVTWTQVAQYIILIA 219 Query: 188 AFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQL 237 A ++P I+ +PQ +G L+E+++GL Q+ Sbjct: 220 AILIPVSMIAHKDGLGWVPQFNYGR-------------LMERVEGLEKQV 256 Score = 179 bits (454), Expect = 3e-49 Identities = 110/308 (35%), Positives = 161/308 (52%), Gaps = 13/308 (4%) Query: 259 LMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETINGP 318 L GTA LPH++ R+ T V AR S GW L F+A+ Y T+P LA + ++ + G Sbjct: 375 LSLGTASLPHILTRYNTTTSVASARRSVGWTLFFVALFYLTVPVLAVLIKYEILTNLVGH 434 Query: 319 ESTGVAYETAPDWIKNWEKT--GLIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATPEI 376 + P W+ W K LI D N DG + ++ E+++ D++VLA PEI Sbjct: 435 H-----FSDLPQWLMQWRKVEPSLISLADTNGDGIVRWS-----EIQMQPDMVVLAAPEI 484 Query: 377 ANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAA 436 A LP + L+AAG LAAALST+ GLLL I+ ++SHD+ P+ S ++ + ++I Sbjct: 485 AGLPYVMSGLIAAGALAAALSTADGLLLTIANALSHDVYYHMVDPNASSQRRVTISKILL 544 Query: 437 ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLL 496 + A Y G + +V AF LAASSLFP +++G+F + + GA+AGMV GL+ Sbjct: 545 LGVALFASYVASLNTGNILFLVGAAFSLAASSLFPVLVLGVFWKRTTRLGAVAGMVAGLV 604 Query: 497 FSASYII-YFKFVNPGDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVD 555 YI+ + F A FGI P G+ G+ F VA VS + Sbjct: 605 VCIYYIVSTYPFFTQMTGFAGPRWFGIEPISSGVFGVPAGFLVAIGVSLIDRKPDAYTRA 664 Query: 556 MVESIRFP 563 +V+ IR P Sbjct: 665 LVDYIRHP 672 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: 1065 Number of extensions: 62 Number of successful extensions: 4 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: 672 Length adjustment: 37 Effective length of query: 535 Effective length of database: 635 Effective search space: 339725 Effective search space used: 339725 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