Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate GFF1281 HP15_1251 sodium: solute symporter family protein
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__Marino:GFF1281 Length = 588 Score = 662 bits (1709), Expect = 0.0 Identities = 339/588 (57%), Positives = 432/588 (73%), Gaps = 26/588 (4%) Query: 6 LTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGI 65 + + VG +F LYI IAIW++AGST +FYVAGGGVHP+ NG A ADWMSAASFIS+AG+ Sbjct: 6 INIIFVGGSFLLYIAIAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGL 65 Query: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAI 125 ++ GY S +LMGWTGGYVLLA+ +APYLRKFGKFTVP+FIGDR+YS+ AR VAV+C I Sbjct: 66 IAAGGYANSTFLMGWTGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLI 125 Query: 126 FICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVL 185 TY+ GQM G GV FSRFLEV+ G+ I VVF YAV+GGMKGITYTQVAQYCVL Sbjct: 126 VASVTYVIGQMAGAGVAFSRFLEVDSTVGLMIAAVVVFVYAVMGGMKGITYTQVAQYCVL 185 Query: 186 IFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFSQYTEG 245 I A+ +PA+FIS+ +TG+ +P LG + VD +G+ +L KL+ + LGF++YT Sbjct: 186 IVAYTIPAVFISLQLTGNPIPGLGLFSTHVD-----SGMPILSKLNQVITDLGFNEYTAD 240 Query: 246 SKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAA 305 +++ T +LM GTAGLPHVI+RFFTVPKV DAR SAGWALVFIA++Y T PA+A+ Sbjct: 241 IDNKLNMVLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVAS 300 Query: 306 FSRVNMIETI--NGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYY--------- 354 +R+N++ TI +G + + Y+ P+WIK WE TGLI++ DKN DG+I Sbjct: 301 MARLNLMTTIYPDGTSAEPIQYDERPNWIKEWEITGLIQFTDKNEDGRIQLYNDSEAFAP 360 Query: 355 ---AKG-ETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSV 410 A+G NE+ ++RDI+VLA PEIANLP WVI L+AAGGLAAALST+AGLLL IS++V Sbjct: 361 TAEARGWNGNELVVNRDILVLANPEIANLPGWVIGLIAAGGLAAALSTAAGLLLAISSAV 420 Query: 411 SHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLF 470 SHDL+K + P IS+K ELL ARI+ A+ IV+A Y G NPPGF A VVA+AFG+AA+SLF Sbjct: 421 SHDLIKGSINPAISEKGELLAARISMAVAIVVATYLGANPPGFAAQVVALAFGIAAASLF 480 Query: 471 PAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPGDNN----ASNWLFGISP 524 PA++MGIFS+ +N GAIAGM+ GL F+ YI +K PG NN NW+ GISP Sbjct: 481 PALMMGIFSKRVNNTGAIAGMLSGLTFTLVYIFVYKGWLFIPGTNNLPDTPDNWVLGISP 540 Query: 525 EGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572 IG +G I+NFAVAFIVS T P + ++VES+R+P+GAG+A DH Sbjct: 541 LSIGAIGAIVNFAVAFIVSNATEEPPVEIQELVESVRYPRGAGQAQDH 588 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: 1072 Number of extensions: 45 Number of successful extensions: 6 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: 588 Length adjustment: 36 Effective length of query: 536 Effective length of database: 552 Effective search space: 295872 Effective search space used: 295872 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