Align actP-like component of D-alanine uptake system (characterized)
to candidate WP_086508553.1 BZY95_RS03245 cation acetate symporter
Query= reanno::psRCH2:GFF346 (589 letters) >NCBI__GCF_002151265.1:WP_086508553.1 Length = 598 Score = 960 bits (2482), Expect = 0.0 Identities = 485/598 (81%), Positives = 521/598 (87%), Gaps = 9/598 (1%) Query: 1 MSQYWINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFI 60 MSQ+ IN+LFVG SF LYIGIA+WARAGSTK+FYVAGGGVHPVTNGMATAADWMSAASFI Sbjct: 1 MSQFAINLLFVGGSFALYIGIAIWARAGSTKDFYVAGGGVHPVTNGMATAADWMSAASFI 60 Query: 61 SMAGLIASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTA 120 SMAGL+ASGGYA S +LMGWTGGYV+LAMLLAPYLRKFGKFTVPDFIGDRFYS+ AR+ A Sbjct: 61 SMAGLLASGGYANSTFLMGWTGGYVILAMLLAPYLRKFGKFTVPDFIGDRFYSKTARVVA 120 Query: 121 VVCLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVA 180 V+CLI+ SVTYVIGQM GAGVAFSRFLEV +S GIWIAA IVF YAVFGGMKGITYTQVA Sbjct: 121 VICLIVASVTYVIGQMTGAGVAFSRFLEVPSSTGIWIAAGIVFLYAVFGGMKGITYTQVA 180 Query: 181 QYIVLIIAYTIPAVFIAMQLTGNPIPMFGMFGTHVDSGVPLLDKLDQVVTDLGFAAYTAD 240 QYIVLIIAYTIPAVFIAMQLTGNPIPMFGMF TH +SGVPLL KLD+VVT LGF YTAD Sbjct: 181 QYIVLIIAYTIPAVFIAMQLTGNPIPMFGMFSTHTESGVPLLAKLDEVVTALGFRDYTAD 240 Query: 241 VDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVAS 300 VDNKLNM LFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGW LVFIALLYLTAPAV S Sbjct: 241 VDNKLNMVLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVGS 300 Query: 301 MARLNLVNTIYPE---------GPQAEAIRYEDRPEWVQTWERTGLIKWEDKNADGRVQM 351 MARLNL TI+PE A I YE+RP+W++TWE TGLI + D+N DGR+QM Sbjct: 301 MARLNLATTIFPEMAGQVEDYQEALANPILYEERPDWIRTWEDTGLITFTDRNNDGRIQM 360 Query: 352 YNDANAKFTPTATERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAA 411 YNDAN F P A+E GW GNELTVNNDI+VLANPEIANLPGWVIGLIAAG IAAALSTAA Sbjct: 361 YNDANPGFQPIASELGWEGNELTVNNDILVLANPEIANLPGWVIGLIAAGGIAAALSTAA 420 Query: 412 GLLLAISSAISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVAL 471 GLLLAISSAISHDLIK INP ISEK EMLAAR+SM AILLAT+LGLNPPGFAAQVVAL Sbjct: 421 GLLLAISSAISHDLIKNTINPSISEKGEMLAARISMAGAILLATYLGLNPPGFAAQVVAL 480 Query: 472 AFGLAAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNT 531 AFG+AAASLFP LMMGIFS R+NSKGA+ GML G+IST +YIF YLGWFFIPGT + N Sbjct: 481 AFGIAAASLFPVLMMGIFSTRMNSKGAICGMLAGLISTLLYIFTYLGWFFIPGTNMLANV 540 Query: 532 PDQWWMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589 W +GISP +FGAVGAM+NFAVAYAVS ATE PPQEIQ+LVESVR PKGAG A H Sbjct: 541 EANWLLGISPLSFGAVGAMINFAVAYAVSSATEEPPQEIQELVESVRYPKGAGAATGH 598 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: 1246 Number of extensions: 41 Number of successful extensions: 2 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: 598 Length adjustment: 37 Effective length of query: 552 Effective length of database: 561 Effective search space: 309672 Effective search space used: 309672 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