Align Phenylacetate permease, Ppa (characterized)
to candidate BWI76_RS02085 BWI76_RS02085 cation acetate symporter
Query= TCDB::O50471 (520 letters) >FitnessBrowser__Koxy:BWI76_RS02085 Length = 549 Score = 727 bits (1876), Expect = 0.0 Identities = 356/519 (68%), Positives = 432/519 (83%), Gaps = 1/519 (0%) Query: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 NW AI MF++FV TL +T WA+ R RS SD+YTAGG +TG QNGLAIAGD +SAASFLG Sbjct: 32 NWQAIIMFLIFVALTLYITYWASKRVRSRSDYYTAGGNITGFQNGLAIAGDFMSAASFLG 91 Query: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 ISA+++ +GYDGL+Y+LG L GWPIILFLIAERLRNLG+YTFADV SYRL Q P+R SA Sbjct: 92 ISALVYTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRTLSA 151 Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181 G+LVV +YL+AQMVGAGKLI+LLFG++Y AV+LVGVLMV YV FGGMLATTWVQIIK Sbjct: 152 CGSLVVVALYLIAQMVGAGKLIQLLFGLNYHIAVVLVGVLMVLYVLFGGMLATTWVQIIK 211 Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 AV+LL G SFMAFMV+KH GFS +F+ A+AVH KG AIM+PGGL+ +P+ A+SLGLG+ Sbjct: 212 AVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGAAIMSPGGLVKDPISALSLGLGL 271 Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYRD 301 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGF+GYFY+L +IGFGAI++VG P+++D Sbjct: 272 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPAFKD 331 Query: 302 ATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361 A G +IGG NM AVHLA AVGGNLFLGFISAVAFATILAVVAGL L+GASAVSHDLYA V Sbjct: 332 AAGQLIGGNNMAAVHLADAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANV 391 Query: 362 IRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421 R+G ATE++E++VS+I L++G++A+LLG++FE+QNIAF+ GL ++AAS NFP++LLS Sbjct: 392 FRKG-ATERQELKVSKITVLILGVVAILLGILFENQNIAFMVGLAFSIAASCNFPIILLS 450 Query: 422 MFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFLS 481 M+W LTTRGA+ G GL +AV+L+VLGP +WV +L HEKA+FPY PALFS+++AF+ Sbjct: 451 MYWSKLTTRGAMIGGWLGLLTAVILMVLGPTIWVQILGHEKAIFPYEYPALFSIAVAFIG 510 Query: 482 AWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 W FS TD+S S ER + AQFIRS TGIG H Sbjct: 511 IWFFSATDNSAEGSRERELFRAQFIRSQTGIGIEKGQAH 549 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: 929 Number of extensions: 39 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: 549 Length adjustment: 35 Effective length of query: 485 Effective length of database: 514 Effective search space: 249290 Effective search space used: 249290 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