Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_035949051.1 N798_RS12935 cation acetate symporter
Query= reanno::PV4:5209923 (572 letters) >NCBI__GCF_000768675.1:WP_035949051.1 Length = 551 Score = 179 bits (454), Expect = 3e-49 Identities = 154/513 (30%), Positives = 237/513 (46%), Gaps = 74/513 (14%) Query: 9 LIVGFTFA-LYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVS 67 + GF L + + + S S EFY A GG NG+A A D++SAASF+ +AG ++ Sbjct: 25 IFAGFVLVTLVVIVKLASGKKSAGEFYTASGGFSGRQNGIAIAGDYLSAASFLGIAGAIA 84 Query: 68 FVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFI 127 GYDG +Y +G+ +++ L +A +R G+ T+ D + R + R + + Sbjct: 85 LQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRLTMADVLSYRLKQRPVRIATATSVLAV 144 Query: 128 CFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVV----FFYAVLGGMKGITYTQVAQYC 183 F Y+ QM G G + S L VE + I +AVV Y ++GGM+G T+ Q+ + Sbjct: 145 SFFYLLAQMAGAGGLVSLLLGVEGEGAQNIVIAVVGIVMIAYVLIGGMRGTTWVQIIKAV 204 Query: 184 VLIFAFMVPAIFISVMMTGHILPQLGFG-AELVDAAGNNTGVYLLEKLDGLSAQLGFSQY 242 +LI A + +MT +L + GF + L DAA N + EKL + G S Sbjct: 205 LLIAA--------TAIMTVWVLGKYGFNLSGLFDAAIQN-NPKVGEKLLEPGVKYGVSTT 255 Query: 243 TEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY--TTI 300 T+ ID ++ AL+ GTAGLPHV+ RF+TVP K AR S WA+ I Y T + Sbjct: 256 TK-----IDFISLSLALVLGTAGLPHVLQRFYTVPTSKQARKSVEWAIWLIGGFYLLTLV 310 Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETN 360 A + V E P G A AP Sbjct: 311 VGYGAGALVGAEEINKAP---GKANAAAP------------------------------- 336 Query: 361 EMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNF- 419 L E+ P + +V+ A L+ AGL + S + +HD+ K+ Sbjct: 337 ----------LLAFELGGSP--FLGIVSGIAFATILAVVAGLTITASATFAHDIYKEVIK 384 Query: 420 MPDISDKQELLYARIAA-ALGI--VMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMG 476 D + E+ ARI+A A+GI ++ G F + +A +VA+AF +AAS+ P I+ Sbjct: 385 RGDTTSDNEVRVARISAVAIGIIAILGGMFAKSQN--IAFLVALAFAVAASANLPTILYS 442 Query: 477 IFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVN 509 +F + N GA+ + GL+ + II+ V+ Sbjct: 443 LFWKRFNTRGALWSIYGGLISTIGLIIFSPVVS 475 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: 797 Number of extensions: 45 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 572 Length of database: 551 Length adjustment: 36 Effective length of query: 536 Effective length of database: 515 Effective search space: 276040 Effective search space used: 276040 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