Align Phenylacetate permease, Ppa (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease
Query= TCDB::O50471 (520 letters) >FitnessBrowser__azobra:AZOBR_RS02940 Length = 572 Score = 694 bits (1790), Expect = 0.0 Identities = 349/539 (64%), Positives = 428/539 (79%), Gaps = 24/539 (4%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 N++AI MF+VFV TL +T WAA RT+SA DFY AGGG+TG QNGLAIAGD +SAASFLG Sbjct: 38 NFSAIVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLG 97 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 I+ +++ +G+DGL++++G L GWPIILFL+AERLRNLGKYTFADV SYR QTP+R +A Sbjct: 98 IAGLVYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAA 157 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 G+L YL+AQMVGAGKLI+LLFG+ YL+AV++VGVLM+AYVTFGGMLATTWVQIIK Sbjct: 158 CGSLATVTFYLIAQMVGAGKLIQLLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIK 217 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 AV+LLSG SFMAF VL FGFS EAMF++AV VH K IMAPG L+++PV AISLG+ + Sbjct: 218 AVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMAL 277 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY+L +IGFGAIV++ D Sbjct: 278 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAIVLLLAP----D 333 Query: 302 ATGA--------------------IIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAV 341 ATGA IIGG NM A+H A AVGG+LF GFISAVAFATILAV Sbjct: 334 ATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGGDLFFGFISAVAFATILAV 393 Query: 342 VAGLALSGASAVSHDLYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAF 401 VAGL L+GASAVSHDLYA VI +G+A+E +E+RVS+I T++IG++++ LG+ FE+QN+AF Sbjct: 394 VAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVIIGIVSIFLGIAFENQNVAF 453 Query: 402 LSGLVLAVAASVNFPVLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHE 461 + GL +AAS NFPVLL+SMFW +TTRGAV G GL S+V L+++GP VW +VL + Sbjct: 454 MVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNP 513 Query: 462 KALFPYSNPALFSMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 ALFPY NP +F++ L+FL+ W FS+TD+S+ A +ER Y AQ+IRS TG+GA GAS H Sbjct: 514 AALFPYDNPGVFTIPLSFLAIWFFSITDNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572 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: 970 Number of extensions: 34 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: 572 Length adjustment: 35 Effective length of query: 485 Effective length of database: 537 Effective search space: 260445 Effective search space used: 260445 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