Align Phenylacetate permease, Ppa (characterized)
to candidate 8499545 DvMF_0315 SSS sodium solute transporter superfamily (RefSeq)
Query= TCDB::O50471 (520 letters) >FitnessBrowser__Miya:8499545 Length = 519 Score = 575 bits (1482), Expect = e-168 Identities = 294/516 (56%), Positives = 378/516 (73%), Gaps = 13/516 (2%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 N +I F +FV FTL VT WAA R+RSA++FY AG +TG QNGLA+AGD +SAASFLG Sbjct: 13 NALSIGFFFLFVAFTLGVTWWAARRSRSAAEFYAAGRSVTGFQNGLALAGDYMSAASFLG 72 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 I+ ++ + GYDGL+Y++G L GWP+++FLIAE LRNLGKYTFADVV+YRL Q P+R+ +A Sbjct: 73 IAGLVALKGYDGLIYSIGFLVGWPVMMFLIAEPLRNLGKYTFADVVAYRLRQRPIRVAAA 132 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 G+L+ YL+AQMVG+G L+ L+FG+ Y AV++VG +M+AYV FGGMLATTWVQIIK Sbjct: 133 CGSLMTVAFYLIAQMVGSGSLVHLMFGLPYETAVLVVGAVMIAYVLFGGMLATTWVQIIK 192 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 AV+LL G S M F VL+HFGFS +F ++ A + G ++APGGL+SNP DA+SLG+ + Sbjct: 193 AVLLLGGASVMVFFVLRHFGFSPAELFRASAARY--GDKVLAPGGLVSNPWDALSLGMAL 250 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301 MFGTAGLPHILMRF+TV DAK ARKSVFYATG I YFY+L +IGFGA+ +VG E Sbjct: 251 MFGTAGLPHILMRFYTVPDAKAARKSVFYATGLISYFYVLTFIIGFGAMTLVGQE----- 305 Query: 302 ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361 GGNM A+ LA+ GG +FLGFI+AVAFATILAVVAGL L+GA+ +HDLYA V Sbjct: 306 VVAGFDKGGNMAALLLAEVTGGTMFLGFIAAVAFATILAVVAGLTLAGATTYAHDLYANV 365 Query: 362 IRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421 R+G++TE +E+R+++ AT+ +G+LAV LG+ F+ QN+AF+ GL A+AAS NFP LL+S Sbjct: 366 FRRGQSTEDDEVRMAKRATVALGVLAVALGIAFKGQNVAFMVGLAFAIAASANFPALLMS 425 Query: 422 MFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHE---KALFPYSNPALFSMSLA 478 + WK +T GAVC G AV L+VL P VWV+VLH A F NPAL S+ A Sbjct: 426 ILWKRFSTFGAVCSIATGATLAVGLIVLSPTVWVDVLHSPWGMAAPFMLKNPALISLPAA 485 Query: 479 FLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGA 514 F + W+ SV A + RY Q IR+ G+GA Sbjct: 486 FAAGWLGSVLRPEPDAEQ---RYAEQKIRNYLGVGA 518 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: 861 Number of extensions: 44 Number of successful extensions: 5 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: 519 Length adjustment: 35 Effective length of query: 485 Effective length of database: 484 Effective search space: 234740 Effective search space used: 234740 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