Align actP-like component of D-alanine uptake system (characterized)
to candidate H281DRAFT_04951 H281DRAFT_04951 cation/acetate symporter
Query= reanno::psRCH2:GFF346 (589 letters) >FitnessBrowser__Burk376:H281DRAFT_04951 Length = 672 Score = 196 bits (497), Expect = 3e-54 Identities = 121/337 (35%), Positives = 174/337 (51%), Gaps = 33/337 (9%) Query: 246 NMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVASMARLN 305 N L L +GTA LPH++ R+ T VA AR S GWTL F+AL Y+T P +A + + Sbjct: 367 NFLSLLLCLSLGTASLPHILTRYNTTTSVASARRSVGWTLFFVALFYVTVPVLAVLIKYE 426 Query: 306 LVNTIYPEGPQAEAIRYEDRPEWVQTWERT--GLIKWEDKNADGRVQMYNDANAKFTPTA 363 ++ + + D P+W+ W + LI D N DG V+ Sbjct: 427 MLTNLVGH-------HFSDLPQWLTQWRKVEPSLITLADTNGDGIVR------------- 466 Query: 364 TERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAISSAISH 423 W+ E+ + D++VLA PEIA LP + GLIAAGA+AAALSTA GLLL I++A+SH Sbjct: 467 ----WS--EIQMQPDMVVLAAPEIAGLPYVMSGLIAAGALAAALSTADGLLLTIANALSH 520 Query: 424 DLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAAASLFPA 483 D+ +++P S + + +++ + L A+++ G +V AF LAA+SLFP Sbjct: 521 DVYYHMVDPGASSQRRVTISKILLLGVALFASYVASLNTGNILFLVGAAFSLAASSLFPV 580 Query: 484 LMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQWWMGISPQA 543 L++G+F KR GAVAGML G++ YI +F A + W GI P + Sbjct: 581 LVLGVFWKRTTRLGAVAGMLAGLLVCIYYIVSTYPFF-----AQMTGFAGPRWFGIEPIS 635 Query: 544 FGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTP 580 G G F VA VS+ P LV+ +R P Sbjct: 636 SGVFGVPAGFLVAIGVSLFDRKPDAYTTALVDYIRHP 672 Score = 180 bits (456), Expect = 2e-49 Identities = 91/193 (47%), Positives = 121/193 (62%) Query: 5 WINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAG 64 WI +F+ +Y I + +R E+YVAG V NGMATAADW+SAASFI +AG Sbjct: 37 WIGYVFLFVPIAVYAVIGLLSRTSDLVEYYVAGRRVPSAFNGMATAADWLSAASFIGLAG 96 Query: 65 LIASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCL 124 I + GY YLMGWTGGY L+A LLAPY+RK ++T+PDF+G RF S R A + Sbjct: 97 SIYATGYDGLAYLMGWTGGYCLVAFLLAPYVRKLARYTIPDFLGTRFSSNAVRGLAALSA 156 Query: 125 ILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVAQYIV 184 IL S Y++ Q+ G G+ +RF+ V + GI+ A + + GGM+ +T+TQVAQYI+ Sbjct: 157 ILCSFVYLVAQIQGVGLIATRFIGVDFAVGIFCGLAGILVCSFLGGMRAVTWTQVAQYII 216 Query: 185 LIIAYTIPAVFIA 197 LI A IP IA Sbjct: 217 LISAILIPVSMIA 229 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: 955 Number of extensions: 49 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 589 Length of database: 672 Length adjustment: 38 Effective length of query: 551 Effective length of database: 634 Effective search space: 349334 Effective search space used: 349334 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