Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_012466706.1 CLIM_RS09040 cation acetate symporter
Query= reanno::PV4:5209923 (572 letters) >NCBI__GCF_000020465.1:WP_012466706.1 Length = 594 Score = 822 bits (2122), Expect = 0.0 Identities = 410/605 (67%), Positives = 489/605 (80%), Gaps = 44/605 (7%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 MDVQT TY+IVG TF +YI IAIW++AGSTKEFYVAG GV P++NGMATAADWMSAASFI Sbjct: 1 MDVQTWTYIIVGATFLIYIAIAIWAKAGSTKEFYVAGAGVPPIINGMATAADWMSAASFI 60 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 S+AG++SF+GYDGSVYLMGWTGGYVLLAL +APYLRKFGKFTVPDF+GDRYYS ARTVA Sbjct: 61 SMAGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNVARTVA 120 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 V+CAIF+ FTY+AGQMRGVGVVFSRFLEV+++TG+ +GM +VFFYAVLGGMKGITYTQVA Sbjct: 121 VICAIFVSFTYVAGQMRGVGVVFSRFLEVDINTGILLGMGIVFFYAVLGGMKGITYTQVA 180 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240 QY VLIFA+MVPAIF+S+M+ G+ +PQ G G AG++ GVYLL+KLDGL QLGF+ Sbjct: 181 QYWVLIFAYMVPAIFLSIMIAGNPIPQFGMG-----GAGSD-GVYLLDKLDGLHQQLGFA 234 Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300 YT GSK MIDVF IT ALM GTAGLPHVIVRFFTVP+V+DAR+SAGWAL+FIA++YTT Sbjct: 235 AYTTGSKPMIDVFAITVALMVGTAGLPHVIVRFFTVPRVRDARISAGWALIFIALLYTTA 294 Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYA----- 355 PA+A F+R+N+I+T++ +Y P W K WEKTGL+ W DKNNDGKI Y Sbjct: 295 PAIATFARLNLIQTVSNN-----SYTDMPGWFKKWEKTGLLAWMDKNNDGKIQYTGKNAG 349 Query: 356 ---------------KGE-------------TNEMKIDRDIMVLATPEIANLPAWVIALV 387 KG+ +NE+ ID+DIMVLA PEI NLP WVIALV Sbjct: 350 GGDPFEGKKPEFTKEKGQHGELLMSNKPTDNSNELFIDKDIMVLANPEIGNLPNWVIALV 409 Query: 388 AAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFG 447 AAGGLAAALST+AGLLLVISTS+SHDL+KK P+IS+K EL+YARIA + IV+AGYFG Sbjct: 410 AAGGLAAALSTAAGLLLVISTSISHDLIKKQINPNISEKGELMYARIAVGVAIVVAGYFG 469 Query: 448 INPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKF 507 INPPGFVA VVA AFGLAA+S FP II+GIFS+ MNKEGAI+GM+ GLLF+A+YI+YFKF Sbjct: 470 INPPGFVAEVVAFAFGLAAASFFPVIILGIFSKRMNKEGAISGMITGLLFTAAYIVYFKF 529 Query: 508 VNPGDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAG 567 ++P N W FGISPEGIG LGM+IN AV+F+VS++T A PQ + ++V+S+R+PKGAG Sbjct: 530 ISPDMNKPEFWWFGISPEGIGTLGMLINVAVSFVVSRITPAPPQEIQELVDSLRYPKGAG 589 Query: 568 EAHDH 572 EA H Sbjct: 590 EASAH 594 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: 1231 Number of extensions: 54 Number of successful extensions: 5 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: 594 Length adjustment: 36 Effective length of query: 536 Effective length of database: 558 Effective search space: 299088 Effective search space used: 299088 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