Align Phenylacetate permease, Ppa (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= TCDB::O50471 (520 letters) >FitnessBrowser__BFirm:BPHYT_RS25605 Length = 516 Score = 425 bits (1093), Expect = e-123 Identities = 230/519 (44%), Positives = 333/519 (64%), Gaps = 21/519 (4%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 M I +FM+ + TL++T WAA RTR+ S+FY AGG L+ +NG A+AGD +SAA+FL Sbjct: 1 MKLLTIVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFL 60 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 G S ++ + G DG LYA+ LA + ++L LIAE +RN G+YTF DV++ R+ + RL + Sbjct: 61 GFSGLVSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLAT 120 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 GT+VV L Y+V QM GAG LI+L+ G+ Y AV+LVG+ M+ YV FGGM+ATTWVQI+ Sbjct: 121 IVGTVVVNLAYMVPQMAGAGALIKLMLGVPYDVAVVLVGIGMIVYVLFGGMIATTWVQIV 180 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KA++LL + M+L F+ A+FAS ++ G ++A GG +P+D +SL + Sbjct: 181 KAMLLLVAACVLVSMLLAAVRFNPLALFASVERLY--GSKMLASGGYFHHPLDTMSLFIS 238 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300 +FG AGLPHI+ RF+TV DA+ ARKSV + G F+++ +IGF + V VG + Sbjct: 239 FIFGVAGLPHIMTRFYTVPDARTARKSVLWLMFLAGSFFMVTTLIGFASAVFVG-----Q 293 Query: 301 DATGAIIGGGNMIAVHLAQ-------AVGGNLFLGFISAVAFATILAVVAGLALSGASAV 353 DA A GGN+ LAQ ++GG +FL I A+AFA ILAVVAGL L+ + A+ Sbjct: 294 DAIRAADKGGNLALPLLAQYLGGGAGSLGGQIFLASICAIAFAAILAVVAGLTLASSGAI 353 Query: 354 SHDLYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASV 413 +HDLY V+R+G ++ E++RV+RIAT+ +G+ A+ L L+ + N+ L L ++VAAS Sbjct: 354 AHDLYVNVLRKGAVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVLVILAISVAASS 413 Query: 414 NFPVLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALF 473 NFP++LLS+FW+ T G + G + GL S+V L +GPA ALFP NPA+ Sbjct: 414 NFPIILLSIFWRRFNTAGVIGGVIGGLTSSVALAFVGPA-----FMGSHALFPIVNPAIV 468 Query: 474 SMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGI 512 S+ + SAW+ T S + G + A ++R+ TGI Sbjct: 469 SLPIGLFSAWL--CTMLSRPTPTQDGDFEAFYLRAQTGI 505 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: 771 Number of extensions: 46 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: 516 Length adjustment: 35 Effective length of query: 485 Effective length of database: 481 Effective search space: 233285 Effective search space used: 233285 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