Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate PP_3272 PP_3272 acetate permease
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__Putida:PP_3272 Length = 520 Score = 721 bits (1861), Expect = 0.0 Identities = 354/519 (68%), Positives = 427/519 (82%), Gaps = 1/519 (0%) Query: 32 NWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGLAIAGDYMSAASFLG 91 NW AI MF++FV FTL +T WA+ R RS SD+YTAGG +TG QNGLAIAGD +SAASFLG Sbjct: 2 NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61 Query: 92 ISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRILSA 151 ISA++F +GYDGL+Y+LG L GWPIILFLIAERLRNLG+YTFADV SYRL Q P+R+ SA Sbjct: 62 ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121 Query: 152 CGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVVLVGVLMMMYVLFGGMLATTWVQIIK 211 G+LVV +YL+AQMVGAGKLIELLFG++Y AV+LVGVLM+ YV FGGMLATTWVQIIK Sbjct: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVSYVTFGGMLATTWVQIIK 181 Query: 212 AVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGVDIMKPGGLVKDPISALSLGLGL 271 AV+LL G SFMAFMV+KH GFS +F+ A+AVH KG IM PGGL+ +P+ A+SLGLG+ Sbjct: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241 Query: 272 MFGTAGLPHILMRFFTVSDAREARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPEYKD 331 MFGTAGLPHILMRFFTVSDA+EARKSVFYATGF+GYFY+L ++GFGAI++VG P Y+D Sbjct: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVVGFGAIVMVGTEPSYRD 301 Query: 332 AAGHLIGGNNMAAVHLANAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANV 391 A G +IGG NM AVHLA AVGGNLFLGFISAVAFATILAVVAGL L+GASAVSHDLYA V Sbjct: 302 ATGAIIGGGNMVAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYACV 361 Query: 392 FKKG-ATEREELRVSKITVLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLS 450 +KG ATE+EE+RVS+I L++G++A+ILG++FE+QNIAF+ GL A+AAS NFP++LLS Sbjct: 362 MRKGKATEQEEMRVSRIATLLIGLLAVILGLMFESQNIAFLSGLVLAVAASVNFPVLLLS 421 Query: 451 MYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQILGHEKAIFPYEYPALFSITVAFLG 510 M+W LTTRGA+ G GL++AV+L++LGP +WV +L +E A+FPY PALFS+++AFL Sbjct: 422 MFWKGLTTRGAVCGSMAGLVSAVLLVVLGPAVWVNVLHNETALFPYSNPALFSMSLAFLS 481 Query: 511 IWFFSATDNSAEGARERELFRAQFIRSQTGFGVEQGRAH 549 W FS TD S ER + QFIRS TG G H Sbjct: 482 AWVFSVTDTSERAVEERGRYLGQFIRSMTGIGAAGASKH 520 Lambda K H 0.329 0.142 0.424 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: 919 Number of extensions: 35 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: 549 Length of database: 520 Length adjustment: 35 Effective length of query: 514 Effective length of database: 485 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