Align Phenylacetate permease, Ppa (characterized)
to candidate 209382 DVU0446 sodium/solute symporter family protein
Query= TCDB::O50471 (520 letters) >MicrobesOnline__882:209382 Length = 515 Score = 563 bits (1452), Expect = e-165 Identities = 289/513 (56%), Positives = 377/513 (73%), Gaps = 10/513 (1%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 N +I F FV FTL +T +AA R+RSAS+FY AG +TG+QNGLA+AGD +SAASFLG Sbjct: 12 NAVSILFFFAFVAFTLAITWFAARRSRSASEFYAAGRSVTGLQNGLALAGDYMSAASFLG 71 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 I+ ++ + GYDGL+Y++G L GWP+++FLIAE LRNLG+YTFADVV+YRL Q P+R+ +A Sbjct: 72 IAGLVSLKGYDGLIYSIGFLVGWPLMMFLIAEPLRNLGRYTFADVVAYRLRQKPIRIAAA 131 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 G+L+ YL+AQMVG+G L++L+FGI Y YAV+ VG +M+AYV FGGMLATTWVQI K Sbjct: 132 CGSLMTVCFYLIAQMVGSGALVQLMFGIRYEYAVVAVGFIMMAYVLFGGMLATTWVQITK 191 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 AV+LL G + M MVL F +S +F +A A H G+A++APGGL+SNP DAISLG+ + Sbjct: 192 AVLLLGGATAMVVMVLAQFDYSPTRLFVTAAAKH--GEAMLAPGGLVSNPWDAISLGMAL 249 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301 MFGTAGLPHILMRF+TV DA+ ARKSVFYATG I YFY+L +IGFGA+++VG D Sbjct: 250 MFGTAGLPHILMRFYTVPDARAARKSVFYATGLISYFYVLTFIIGFGAMMLVGP-----D 304 Query: 302 ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361 A GGNM A LA+ GG +FLGFI+AVAFATILAVVAGL L+GA+ SHDLYA V Sbjct: 305 AIRMFDKGGNMAAPLLAEVTGGTMFLGFIAAVAFATILAVVAGLTLAGATTFSHDLYANV 364 Query: 362 IRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421 + G++ E +E+RV++ AT+ +G++A+LLG+ F+ QN+AF+ GL A+AAS N P LLLS Sbjct: 365 FKGGQSNEADEVRVAKRATIALGVIAMLLGIAFKGQNVAFMVGLAFAIAASANLPALLLS 424 Query: 422 MFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFLS 481 + W+G +T GAV + G AV L+++ P VW +V H A FP NPAL SM AF++ Sbjct: 425 IMWRGCSTTGAVWAIVTGGVLAVGLIIVSPTVWTDVFHLGTAPFPLKNPALLSMPAAFMA 484 Query: 482 AWVFSVTDSSERASEERGRYLAQFIRSMTGIGA 514 S+ SEE R+ AQ IR+ G+GA Sbjct: 485 GIAGSLLRPD---SEESARFDAQKIRNYLGVGA 514 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: 833 Number of extensions: 54 Number of successful extensions: 6 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: 520 Length of database: 515 Length adjustment: 35 Effective length of query: 485 Effective length of database: 480 Effective search space: 232800 Effective search space used: 232800 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