Align actP-like component of D-alanine uptake system (characterized)
to candidate RR42_RS13875 RR42_RS13875 sodium:solute symporter
Query= reanno::psRCH2:GFF346 (589 letters) >FitnessBrowser__Cup4G11:RR42_RS13875 Length = 683 Score = 195 bits (495), Expect = 6e-54 Identities = 130/341 (38%), Positives = 179/341 (52%), Gaps = 41/341 (12%) Query: 244 KLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVASMAR 303 +LN L LM+GTA LPH++ R +T P V ++R S W + FIALLY++APA+A++ + Sbjct: 376 RLNFVLLVFCLMLGTASLPHILTRLYTTPSVKESRNSVAWAVFFIALLYVSAPALAALVK 435 Query: 304 L----NLVNTIYPEGPQAEAIRYEDRPEWVQTWERTG--LIKWEDKNADGRVQMYNDANA 357 +LV T Y E PQ WV W + + D N DG VQ Sbjct: 436 YEFFQHLVGTPYAELPQ-----------WVVQWRKVDPPVFGIRDVNGDGIVQ------- 477 Query: 358 KFTPTATERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAI 417 W E+ + D+IVLA PEIA LP + GL+AAGA+AAALSTA GLLL I Sbjct: 478 ----------WA--EILIQPDMIVLAAPEIAGLPYVISGLVAAGALAAALSTADGLLLTI 525 Query: 418 SSAISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAA 477 ++A+SHD+ + + S + + A++ + L A+++ PG +V AF LAA Sbjct: 526 ANALSHDVFYHMGDRTASHQRRVTTAKIVLLGVALFASYVTSLRPGNILFLVGAAFSLAA 585 Query: 478 ASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQWWM 537 +S FP L++ IF +R + GAVAGM+ G+ YIF+ FF T N W Sbjct: 586 SSFFPVLVLAIFWRRTTAAGAVAGMVAGLGVAVYYIFVNYP-FFTRMTGIFGNR----WF 640 Query: 538 GISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVR 578 G+ P A GA G FAVA VS+ T I LV +R Sbjct: 641 GVDPIASGAFGVPAGFAVAILVSLLTPRNAPVIDRLVTYLR 681 Score = 171 bits (434), Expect = 7e-47 Identities = 93/229 (40%), Positives = 133/229 (58%), Gaps = 16/229 (6%) Query: 5 WINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAG 64 W+ +F+ + +Y I + R E+YVAG V + NGMA AADWMSAASFI +AG Sbjct: 42 WLGYVFLFVTIAIYACIGLICRTSDLNEYYVAGRRVPALFNGMAIAADWMSAASFIGLAG 101 Query: 65 LIASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRG-------AR 117 ++ + GY Y+MGWTGGY L+A LLAPYLRK+G +T+PDF+ R Y G R Sbjct: 102 ILFASGYEGLAYVMGWTGGYCLVAFLLAPYLRKYGGYTIPDFLAAR-YGNGKPGGNMPVR 160 Query: 118 LTAVVCLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYT 177 AV+ L S Y++ Q+ G G+ +RF+ V + G++ A + + GGM+ +T+T Sbjct: 161 AIAVMAASLCSFVYLVAQIQGVGLIVTRFIGVEFAVGVFFGLAGILVCSFLGGMRAVTWT 220 Query: 178 QVAQYIVLIIAYTIPAVFIAMQLTGNPIPMFGMFGTHVDSGVPLLDKLD 226 QVAQYI+LI A+ + IA + +P +GT LL +LD Sbjct: 221 QVAQYIMLIAAFLVTVSMIAWKHHHEALPQLS-YGT-------LLQQLD 261 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: 1030 Number of extensions: 53 Number of successful extensions: 6 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: 683 Length adjustment: 38 Effective length of query: 551 Effective length of database: 645 Effective search space: 355395 Effective search space used: 355395 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