Align actP-like component of D-alanine uptake system (characterized)
to candidate 201983 SO2857 sodium/solute symporter family protein (NCBI ptt file)
Query= reanno::psRCH2:GFF346 (589 letters) >FitnessBrowser__MR1:201983 Length = 578 Score = 683 bits (1762), Expect = 0.0 Identities = 344/590 (58%), Positives = 437/590 (74%), Gaps = 23/590 (3%) Query: 6 INMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAGL 65 + L VG SF LYIGIA+W RAGSTKEFYVAGGGVHPV NGMATAADWMSAASFIS+AG+ Sbjct: 6 LTYLIVGLSFALYIGIALWTRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFISLAGI 65 Query: 66 IASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCLI 125 ++ GY SVYLMGWTGGYVLLA+ +APYLRKFGKFTVPDF+G+R+YS+ AR AV+C I Sbjct: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFLGERYYSQAARTVAVICAI 125 Query: 126 LISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVAQYIVL 185 I TY+ GQM G GV FSRFLEV G++I A+VF Y+V GGMKGITYTQVAQY VL Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYSVLGGMKGITYTQVAQYCVL 185 Query: 186 IIAYTIPAVFIAMQLTGNPIPMFGMFGTHV------DSGVPLLDKLDQVVTDLGFAAYTA 239 I A+ +PA+F+++ +TG+ IP G FG + +SGV LLDKL+ + DLGFA YT Sbjct: 186 IFAFMVPAIFLSVMMTGHIIPQIG-FGAQLLDAAGNNSGVYLLDKLNNLSVDLGFAPYTD 244 Query: 240 DVDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVA 299 + +++ T +LM+GTAGLPHVI+RFFTVPKV DAR SAGW LVFIA++Y T PA+A Sbjct: 245 GSKSMIDVLCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTVPALA 304 Query: 300 SMARLNLVNTIYPEGPQAEAIRYEDRPEWVQTWERTGLIKWEDKNADGRVQMYNDANAKF 359 + +R+N++ TI GP + + YE P W++ WE+TGLIKW+DKN DG++ A K Sbjct: 305 AFSRVNMIETI--NGPDQKGVAYETAPNWIKNWEKTGLIKWDDKNGDGKIYY---ATGKI 359 Query: 360 TPTATERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAISS 419 A+ NE+ ++NDIIVLA PEIANLP WVI L+AAG +AAALST+AGLLL IS+ Sbjct: 360 EDAAST-----NEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVIST 414 Query: 420 AISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAAAS 479 ++SHDL+K + P IS+K E++ ARL+ I++A + G+NPPGF A VVA AFGLAA+S Sbjct: 415 SVSHDLLKKNLMPNISDKKELMYARLAAGIGIVIAGYFGVNPPGFVAAVVAFAFGLAASS 474 Query: 480 LFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQWWMGI 539 LFPA++MGIFSK +N +GA+AGM++G+ T+ YI + FI TA N P W++GI Sbjct: 475 LFPAIIMGIFSKTMNKEGAIAGMILGLFFTSGYIVYFK---FIDPTA---NVPANWFLGI 528 Query: 540 SPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589 SP+ G VG ++NF VA VS T A P +Q++VES+R PKGAG A DH Sbjct: 529 SPEGIGMVGMVINFVVAAIVSKVTAATPVHVQEMVESIRFPKGAGEASDH 578 Lambda K H 0.324 0.137 0.419 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: 1050 Number of extensions: 37 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: 589 Length of database: 578 Length adjustment: 36 Effective length of query: 553 Effective length of database: 542 Effective search space: 299726 Effective search space used: 299726 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