Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__BFirm:BPHYT_RS25605 Length = 516 Score = 174 bits (442), Expect = 6e-48 Identities = 145/520 (27%), Positives = 230/520 (44%), Gaps = 81/520 (15%) Query: 3 VQTLTYLIVGFTFALYIGIAIWS--RAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 ++ LT +I A+ + I W+ R +T EFY AGG + NG A A DWMSAA+F+ Sbjct: 1 MKLLTIVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFL 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 +G+VS G DGS+Y + ++++ + +A +R G++T D I +R AR Sbjct: 61 GFSGLVSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLAT 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 +V + + Y+ QM G G + L V D V + + Y + GGM T+ Q+ Sbjct: 121 IVGTVVVNLAYMVPQMAGAGALIKLMLGVPYDVAVVLVGIGMIVYVLFGGMIATTWVQIV 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNN---TGVYLLEKLDGLSAQL 237 + +L+ A + +S+++ L A + G+ +G Y LD +S + Sbjct: 181 KAMLLLVA---ACVLVSMLLAAVRFNPLALFASVERLYGSKMLASGGYFHHPLDTMSLFI 237 Query: 238 GFSQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY 297 F +FG AGLPH++ RF+TVP + AR S W L+F+A + Sbjct: 238 SF--------------------IFGVAGLPHIMTRFYTVPDARTARKSVLW-LMFLAGSF 276 Query: 298 TTIPALAAFSRVNMI--ETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYA 355 + L F+ + + I + G A + + G + G+I+ A Sbjct: 277 FMVTTLIGFASAVFVGQDAIRAADKGG---NLALPLLAQYLGGGA-----GSLGGQIFLA 328 Query: 356 KGETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDL- 414 + A AA L+ AGL L S +++HDL Sbjct: 329 S------------------------------ICAIAFAAILAVVAGLTLASSGAIAHDLY 358 Query: 415 ---LKKNFMPDISDKQELLYARIA-AALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLF 470 L+K +SD +++ ARIA A+GI G + V +V +A +AASS F Sbjct: 359 VNVLRKG---AVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVLVILAISVAASSNF 415 Query: 471 PAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNP 510 P I++ IF R N G I G++ GL S + FV P Sbjct: 416 PIILLSIFWRRFNTAGVIGGVIGGLTSS----VALAFVGP 451 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: 776 Number of extensions: 41 Number of successful extensions: 3 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: 516 Length adjustment: 35 Effective length of query: 537 Effective length of database: 481 Effective search space: 258297 Effective search space used: 258297 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: 52 (24.6 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