Align actP-like component of D-alanine uptake system (characterized)
to candidate Ac3H11_204 Acetate permease ActP (cation/acetate symporter)
Query= reanno::psRCH2:GFF346 (589 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_204 Length = 699 Score = 187 bits (474), Expect = 2e-51 Identities = 98/233 (42%), Positives = 145/233 (62%), Gaps = 10/233 (4%) Query: 1 MSQYWINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFI 60 +S++WI +F+ + ++Y GI V+ R +++YVAG + P+ NGMATAADWMSAASFI Sbjct: 45 LSRHWIGPIFLFLTVMVYAGIGVYGRTTDPEDYYVAGRRIPPMYNGMATAADWMSAASFI 104 Query: 61 SMAGLIASGGYATS-------VYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYS 113 S++G + G++ + YL+GWTGG+ L+AML+AP+LR G +T+PDF RF Sbjct: 105 SLSGALYLQGFSGTPGQAGGLAYLLGWTGGFCLVAMLIAPHLRAMGLYTIPDFFHVRFGG 164 Query: 114 RGARLTAVVCLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKG 173 R R+ A + +L S TYV+ Q+ G G+ SR V GI + V + GGM+ Sbjct: 165 RWPRVIAALAAVLCSFTYVVAQIYGVGLIASRLTGVQFEIGIMLGLGGVLLCSFLGGMRA 224 Query: 174 ITYTQVAQYIVLIIAYTIPAVFIAMQLTGNPIP--MFG-MFGTHVDSGVPLLD 223 IT+TQVAQY+VL++A+ IP ++A + GNP+ ++G G D LLD Sbjct: 225 ITWTQVAQYVVLLLAFMIPVSWLAYKQLGNPLAPLVYGEQIGKIADLEAQLLD 277 Score = 182 bits (462), Expect = 4e-50 Identities = 118/327 (36%), Positives = 169/327 (51%), Gaps = 36/327 (11%) Query: 246 NMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVASMARLN 305 N LM+GTAGLPH++ RF+T P V+ AR S GW+L FIALLYL+APA+A + + Sbjct: 395 NFLALMFCLMVGTAGLPHLLTRFYTSPSVSAARASVGWSLFFIALLYLSAPALAVLVKFE 454 Query: 306 LVNTIYPEGPQAEAIRYEDRPEWVQTWER--TGLIKWEDKNADGRVQMYNDANAKFTPTA 363 ++ + G EA+ P W+ W R + L+ ED N DG +Q Sbjct: 455 VMQNLV--GSSFEAL-----PTWMAQWSRVDSSLLSLEDVNGDGLIQF------------ 495 Query: 364 TERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAISSAISH 423 E+ + D+I+LA PE+ LP V GL+AAG +AAALSTA GLLL IS+A+ Sbjct: 496 -------GEIRLGADLIMLATPELGGLPYVVSGLVAAGGLAAALSTADGLLLTISNALVR 548 Query: 424 DLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAAASLFPA 483 DL K S + ++ ++ ++ A L A ++ P +V+ +F LAA++ PA Sbjct: 549 DLYFQDSQRKASPEQRVILSKFALLAVALSAAFVAALKPSEILPMVSASFSLAASAFVPA 608 Query: 484 LMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASI-PN--TPDQWWMGIS 540 +++GIF + +GAVAGML G + AVY L +P + P D W GI Sbjct: 609 MVLGIFWRGTTRQGAVAGMLTG-LGIAVYYML----SHVPAVQGVLPRWLLADGLWFGIQ 663 Query: 541 PQAFGAVGAMLNFAVAYAVSMATEAPP 567 P + G G V +S T P Sbjct: 664 PISAGVFGVPCGLLVTVVLSWMTRPAP 690 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: 1035 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 589 Length of database: 699 Length adjustment: 38 Effective length of query: 551 Effective length of database: 661 Effective search space: 364211 Effective search space used: 364211 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: 54 (25.4 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