Align Phenylacetate permease, Ppa (characterized)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily
Query= TCDB::O50471 (520 letters) >FitnessBrowser__Cola:Echvi_1267 Length = 567 Score = 162 bits (411), Expect = 2e-44 Identities = 152/583 (26%), Positives = 260/583 (44%), Gaps = 90/583 (15%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 + WT I + + F + + + W+ R S +FY AGGG++ + NG+A D +SAASF+ Sbjct: 4 LTWTYILVGLSFALY-IGIAIWS--RAGSTKEFYVAGGGVSPLANGMATGADWMSAASFI 60 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 ++ ++ GYDG +Y +G G+ ++ L+A LR GK+T D V R R+ + Sbjct: 61 SMAGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVA 120 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 F + ++ Y+ QM G G + + V++ ++ Y GGM T+ Q+ Sbjct: 121 VFCAIFISFTYVAGQMRGVGIVFSRYLEVDINTGVIIGMCIVFFYAVLGGMKGITYTQVA 180 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 + +L+ AFMV F + + ++ + G + A G L + +D + LG Sbjct: 181 QYCVLI-----FAFMVPAI--FISMQLTSNPIPQLGLGGTV-ADGTYLLDKLDGVLTDLG 232 Query: 241 --------------------MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYL 280 +M GTAGLPH+++RFFTV K+AR S YA FI Y Sbjct: 233 FHAYTSGKKSMGDMFAITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYT 292 Query: 281 LLIVIG----FGAIVMVGTEP-------------------SYRDATGAI----------- 306 + + AI V +P + ++ G + Sbjct: 293 TAPAVSAFGIYNAIDSVSEKPIDDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPERNEF 352 Query: 307 -IGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACVIRQG 365 I M+ + A N +G ++A A L+ AGL L +++VS DL A G Sbjct: 353 TIDKDIMVLANPEIAQLPNWVVGLVAAGGMAAALSTAAGLLLVISTSVSRDL-AKNFNPG 411 Query: 366 KATEQEEMRVSRIATLLIGLLAVLLGLM---FESQNIAFLSGLVLAVAASVNFPVLLLSM 422 ++++E+ ++R+A + ++A G+ F ++ +AF GL AA+ FPV+++ + Sbjct: 412 -ISDKKELLIARVAAAVAVIVAGYFGVNPPGFVAEVVAFAFGL----AAASFFPVIIMGI 466 Query: 423 FWKGLTTRGAVCGSMAGLASAVLLVVLG---------PAVWVNVLHHEKALFPYSNPALF 473 F K + GA+ G + GL + ++ PA + H + P ++ Sbjct: 467 FSKRMNKEGAIWGMLVGLVFTLSYIIYFKFGTDLFGIPAESLTAEHWWFGISPEGIGSI- 525 Query: 474 SMSLAFLSAWVFS-VTDSSERASEERGRYLAQFIRSMTGIGAA 515 M L FL ++V S VT + A +E + + IR G G A Sbjct: 526 GMVLNFLVSFVVSRVTPAPPEAVQE----MVEDIRIPRGAGQA 564 Lambda K H 0.328 0.139 0.407 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: 783 Number of extensions: 52 Number of successful extensions: 3 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: 520 Length of database: 567 Length adjustment: 35 Effective length of query: 485 Effective length of database: 532 Effective search space: 258020 Effective search space used: 258020 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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