Align Phenylacetate permease, Ppa (characterized)
to candidate PfGW456L13_2421 Acetate permease ActP (cation/acetate symporter)
Query= TCDB::O50471 (520 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421 Length = 548 Score = 915 bits (2364), Expect = 0.0 Identities = 463/520 (89%), Positives = 496/520 (95%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 +NW AI MF+VFV FTL VTRWAALRTRS SDFYTAGGG+TG QNGLAIAGDMISAASFL Sbjct: 29 LNWNAIGMFLVFVLFTLGVTRWAALRTRSTSDFYTAGGGMTGFQNGLAIAGDMISAASFL 88 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 GISAMMF+NGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRL QTPVRLTS Sbjct: 89 GISAMMFLNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLEQTPVRLTS 148 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 AFGTL VALMYLVAQMVGAGKLIELLFGI YLYAVMLVGVLMV YVTFGGMLATTWVQII Sbjct: 149 AFGTLTVALMYLVAQMVGAGKLIELLFGIDYLYAVMLVGVLMVFYVTFGGMLATTWVQII 208 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KAVMLL GTSFMAFMVLKHFGFSTEAMFA A AVHAKG AIMAPGGLLSNP+DAISLGLG Sbjct: 209 KAVMLLFGTSFMAFMVLKHFGFSTEAMFAGATAVHAKGNAIMAPGGLLSNPIDAISLGLG 268 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLI++GFGAIVMVGT+P++R Sbjct: 269 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIIVGFGAIVMVGTDPAFR 328 Query: 301 DATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360 DA+GAIIGGGNM+AVHLA AVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC Sbjct: 329 DASGAIIGGGNMVAVHLAHAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 388 Query: 361 VIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420 V+R+G+A+EQ+EMRVSRIATL IG+LA++LGL+FESQNIAFLSGLVLA+AASVNFPVL L Sbjct: 389 VMRKGQASEQQEMRVSRIATLCIGVLAIVLGLLFESQNIAFLSGLVLAIAASVNFPVLFL 448 Query: 421 SMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFL 480 SM+WKGLTTRGAV GS++GL SA++L+VL PAVWVNV+HH+KALFPYSNPALFSMSLAF Sbjct: 449 SMYWKGLTTRGAVLGSLSGLVSAIVLLVLSPAVWVNVMHHDKALFPYSNPALFSMSLAFF 508 Query: 481 SAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 SAW+FSVTD+S RA+ ERGRYLAQFIRSMTGIGA GASKH Sbjct: 509 SAWLFSVTDTSPRAALERGRYLAQFIRSMTGIGATGASKH 548 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: 1075 Number of extensions: 29 Number of successful extensions: 2 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: 548 Length adjustment: 35 Effective length of query: 485 Effective length of database: 513 Effective search space: 248805 Effective search space used: 248805 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