Align actP-like component of D-alanine uptake system (characterized)
to candidate 6937353 Sama_1523 sodium/solute symporter family protein (RefSeq)
Query= reanno::psRCH2:GFF346 (589 letters) >FitnessBrowser__SB2B:6937353 Length = 572 Score = 674 bits (1740), Expect = 0.0 Identities = 339/589 (57%), Positives = 431/589 (73%), Gaps = 27/589 (4%) Query: 6 INMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAGL 65 + L VG SF LYIGIA+W+RAGSTKEFYVAGGGV PV NGMATAADWMSAASFIS+AG+ Sbjct: 6 LTYLIVGLSFALYIGIAIWSRAGSTKEFYVAGGGVPPVMNGMATAADWMSAASFISLAGI 65 Query: 66 IASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCLI 125 ++ GY SVYLMGWTGGYVLLA+ +APYLRKFGKFTVPDFIG+R+YS+ AR AVVC I Sbjct: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGERYYSQAARTVAVVCAI 125 Query: 126 LISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVAQYIVL 185 I TY+ GQM G GV FSRFLEV G++I A+VF YAV GGMKGITYTQVAQY VL Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVDVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVL 185 Query: 186 IIAYTIPAVFIAMQLTGNPIPMFGMFGTHVD-----SGVPLLDKLDQVVTDLGFAAYTAD 240 I A+ +PA+FI++ +TG+ IP G +D +GV LLDKLD + T+LGF+ YT Sbjct: 186 IFAFMVPAIFISVMMTGHIIPQLGFGAELIDAAGNGTGVYLLDKLDGLSTELGFSQYTEG 245 Query: 241 VDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVAS 300 + +++F T +LM+GTAGLPHVI+RFFTVP+V DAR SAGW LVFIA++Y T PA+A+ Sbjct: 246 SKSMIDVFAITAALMVGTAGLPHVIVRFFTVPRVKDARSSAGWALVFIAIMYTTVPALAA 305 Query: 301 MARLNLVNTIYPEGPQAEAIRYEDRPEWVQTWERTGLIKWEDKNADGRVQMYNDANAKFT 360 +R+N++ TI GP + + YE P W++ WE+TGLIKW+DKN DG++ Y +A Sbjct: 306 FSRVNMIETI--NGPDSTGVAYETAPGWIKNWEKTGLIKWDDKNGDGKM-YYTKGDA--- 359 Query: 361 PTATERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAISSA 420 NE+ ++ DI+VLA PEIANLP WVI L+AAG +AAALST+AGLLL IS++ Sbjct: 360 ----------NEMNIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTS 409 Query: 421 ISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAAASL 480 +SHDL+K P IS+K E+L AR++ I++A + G+NPPGF A VVA AFGLAA+SL Sbjct: 410 VSHDLMKKGFAPNISDKQELLYARIAAAVGIVIAGYFGINPPGFVAAVVAFAFGLAASSL 469 Query: 481 FPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQWWMGIS 540 FPA++MGIFSK++N +GA+AGM+VG+ TA YI + F P N P W GIS Sbjct: 470 FPAIVMGIFSKKMNKEGAIAGMVVGLGFTAAYIVYFK--FVNPAA----NVPANWLFGIS 523 Query: 541 PQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589 P+ G +G ++NFAVA V+ T A P ++++VE +R PKGAG A DH Sbjct: 524 PEGIGMIGMLINFAVAVIVAKLTSAVPAHVEEMVEGIRFPKGAGGAQDH 572 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: 1070 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: 589 Length of database: 572 Length adjustment: 36 Effective length of query: 553 Effective length of database: 536 Effective search space: 296408 Effective search space used: 296408 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