Align Phenylacetate permease, Ppa (characterized)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter
Query= TCDB::O50471 (520 letters) >NCBI__GCF_000009985.1:WP_011386681.1 Length = 554 Score = 681 bits (1757), Expect = 0.0 Identities = 341/519 (65%), Positives = 419/519 (80%), Gaps = 1/519 (0%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 NW AI MF+ FV TL +T WA+ RT+SA+DFYTAGGG+TG QNGLAIAGD +SAASFLG Sbjct: 37 NWHAILMFVGFVLLTLGITWWASKRTKSAADFYTAGGGITGFQNGLAIAGDFMSAASFLG 96 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 ++A+++ G DG++YA+GV+ GWP++LFLIAE LRNLGKYTFADVV+YRLA+ PVR +A Sbjct: 97 VTALLYGTGLDGMVYAVGVVVGWPLMLFLIAEPLRNLGKYTFADVVAYRLAKVPVRTYAA 156 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 F +L V + YL+AQMVGAG+LI+LLFG+ YLYA+ LVG LM+ YVTFGGM ATTWVQIIK Sbjct: 157 FSSLTVVVFYLIAQMVGAGQLIKLLFGMDYLYALFLVGGLMMIYVTFGGMAATTWVQIIK 216 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 AV+LLSG +FMA VL FGFS EAMFA AV V AIM+PG L +P+D ISL + + Sbjct: 217 AVLLLSGATFMAGAVLSRFGFSPEAMFAKAVQVKGSN-AIMSPGLLFKDPIDTISLAMAL 275 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301 FGTAGLPHILMRFFTV DAKEARKSVFYAT FIG+FY+L +VIG GAI +V T+P+Y Sbjct: 276 AFGTAGLPHILMRFFTVPDAKEARKSVFYATAFIGFFYVLAVVIGIGAIALVATDPTYLA 335 Query: 302 ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361 A+ GGGNM AV LA AVGG+LFLGFISAVAFATILAVVAGL L+GASA+SHDLYA V Sbjct: 336 DGKALKGGGNMAAVWLAHAVGGDLFLGFISAVAFATILAVVAGLTLAGASAISHDLYANV 395 Query: 362 IRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421 +G A E+ E+R+SR+A+L +G++A++LG++FE QNIA+L+GL LA+AAS NFP+LLLS Sbjct: 396 FARGHAKEETELRISRLASLALGVIAIILGMLFEKQNIAYLAGLTLAIAASANFPLLLLS 455 Query: 422 MFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFLS 481 M W GLT+RGA+ G +AGL SAV+L VLGPAVW VL + + +FP+ NPALFS++ F + Sbjct: 456 MLWPGLTSRGAILGGVAGLVSAVVLTVLGPAVWKAVLGNPQPIFPWGNPALFSVAAGFAA 515 Query: 482 AWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 W FSVTD SERA E+ + AQF+RS TG+GA G S H Sbjct: 516 TWFFSVTDGSERAVREKAEFNAQFVRSQTGLGAEGVSAH 554 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: 941 Number of extensions: 45 Number of successful extensions: 4 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: 554 Length adjustment: 35 Effective length of query: 485 Effective length of database: 519 Effective search space: 251715 Effective search space used: 251715 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