Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_072906607.1 BUB13_RS05645 cation acetate symporter
Query= reanno::PV4:5209923 (572 letters) >NCBI__GCF_900142125.1:WP_072906607.1 Length = 600 Score = 681 bits (1757), Expect = 0.0 Identities = 349/598 (58%), Positives = 432/598 (72%), Gaps = 37/598 (6%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 M +Q LTYL+VG TFALYIGIAIW+RAGST EFY AGG VHPV+NGMAT ADWMSAASFI Sbjct: 1 MGLQALTYLVVGLTFALYIGIAIWARAGSTSEFYAAGGSVHPVLNGMATGADWMSAASFI 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 S+AG++ GY G+V+LMGWTGGYVLLA+ +APYLRKFGKFTVP F RYYS+ A TV Sbjct: 61 SMAGLIGLFGYGGTVFLMGWTGGYVLLAMLLAPYLRKFGKFTVPSFFSARYYSKGAGTVG 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 VVC + TYI GQM GVGV FSRFL V TG++IGM +VF YAV GGMKGITYTQVA Sbjct: 121 VVCLLIASLTYIIGQMTGVGVAFSRFLGVSNATGIFIGMGIVFMYAVFGGMKGITYTQVA 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240 QYCVLI A+ VPAIFIS+ +TG+ +PQLG G+++ T V LL KLD + LGF+ Sbjct: 181 QYCVLILAYTVPAIFISLNLTGNPIPQLGLGSDMA-----GTDVALLSKLDQVVTDLGFA 235 Query: 241 QYTEGSKG-MIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT 299 QYT +G M++ F T +LM GTAGLPHVI+RFFTVP VKDAR SAGWALVFIAI+YTT Sbjct: 236 QYTTNFRGSMLNTFVYTLSLMIGTAGLPHVIMRFFTVPTVKDARSSAGWALVFIAILYTT 295 Query: 300 IPALAAFSRVNMIETING-----------PESTGVAYETAPDWIKNWEKTGLIKWDDKNN 348 PA+AA + +N+ T+N + + Y+ P W+K WE TGL+K+ DKN Sbjct: 296 APAVAAMATMNLHATVNPGIVQDANFDVMAPGSQIVYDERPAWMKRWEVTGLLKFTDKNG 355 Query: 349 DGKIYYAKGET------------NEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAAL 396 DG+I + ++ NE+ +++DIMVLA PEIA LP WVIALVAAGGLAAAL Sbjct: 356 DGRIQHYNDKSKDPKFAAAGWAGNELSVNKDIMVLANPEIALLPNWVIALVAAGGLAAAL 415 Query: 397 STSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAA 456 ST+AGLLL IS+++SHDL+K+ MPDIS+K EL+ +I+ A I +AGY G+NPP F A Sbjct: 416 STAAGLLLAISSAISHDLIKEKLMPDISEKGELMAGKISMACSICVAGYLGLNPPDFAAG 475 Query: 457 VVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK---FVNPGD- 512 VAIAFGLAASS+FPA++MGIFS+TMNKEGAIAGM+ G+ + Y+ K F+ + Sbjct: 476 TVAIAFGLAASSIFPALMMGIFSKTMNKEGAIAGMLAGIGVTMLYVFAHKGIFFIKGTEF 535 Query: 513 ----NNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGA 566 S++ FGI P G +G ++NFAVAF V +T VP+N+ MVE +R PKG+ Sbjct: 536 LGLFGGKSSFFFGIEPNAFGAVGAVVNFAVAFAVKNMTTPVPENIAQMVEDVRIPKGS 593 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: 1150 Number of extensions: 54 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 572 Length of database: 600 Length adjustment: 37 Effective length of query: 535 Effective length of database: 563 Effective search space: 301205 Effective search space used: 301205 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 24 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