Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate PP_3272 PP_3272 acetate permease
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__Putida:PP_3272 Length = 520 Score = 724 bits (1870), Expect = 0.0 Identities = 354/520 (68%), Positives = 434/520 (83%) Query: 33 LNVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGKITGFQNGLAIAGDYMSAASFL 92 +N +AI MF+VFV TL +T WA+ R +SA+D+Y AGG +TG QNGLAIAGD +SAASFL Sbjct: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 Query: 93 GISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVASYRLGQTQIRSLS 152 GISA+++ +GYDGL+Y++G L GWPIILFLIAERLRNLGKYTFADV SYRL QT +R S Sbjct: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 Query: 153 ACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVGILMVLYVLFGGMLATTWVQII 212 A G+LVV YL+AQMVGAGKLI+LLFG+ Y AV+LVG+LMV YV FGGMLATTWVQII Sbjct: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVSYVTFGGMLATTWVQII 180 Query: 213 KAVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGEAIMSPGGLVKDPISAFSLGLA 272 KAV+LLSG SFMA MV+KH F A+F+ A+ VH KG+AIM+PGGL+ +P+ A SLGL Sbjct: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 Query: 273 LMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAILLVSTNPAFK 332 +MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFY+L ++GFGAI++V T P+++ Sbjct: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVVGFGAIVMVGTEPSYR 300 Query: 333 DAAGALMGGNNMAAVHLANAVGGSIFLGFISAVAFATILAVVAGLTLAGASAVSHDLYAS 392 DA GA++GG NM AVHLA AVGG++FLGFISAVAFATILAVVAGL L+GASAVSHDLYA Sbjct: 301 DATGAIIGGGNMVAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360 Query: 393 VIKKGKANDKDEIRVSKITTIALGVLAIGLGILFESQNIAFMVGLAFSIAASCNFPVLLL 452 V++KGKA +++E+RVS+I T+ +G+LA+ LG++FESQNIAF+ GL ++AAS NFPVLLL Sbjct: 361 VMRKGKATEQEEMRVSRIATLLIGLLAVILGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420 Query: 453 SMYWKNLTTRGAMIGGWLGLVSAVGLMVLGPTIWVSILHHEKAIFPYEYPALFSMIIAFV 512 SM+WK LTTRGA+ G GLVSAV L+VLGP +WV++LH+E A+FPY PALFSM +AF+ Sbjct: 421 SMFWKGLTTRGAVCGSMAGLVSAVLLVVLGPAVWVNVLHNETALFPYSNPALFSMSLAFL 480 Query: 513 GIWFFSITDKSSAAEKERALYFPQFVRSQTGLGSSGAVSH 552 W FS+TD S A +ER Y QF+RS TG+G++GA H Sbjct: 481 SAWVFSVTDTSERAVEERGRYLGQFIRSMTGIGAAGASKH 520 Lambda K H 0.327 0.140 0.415 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: 953 Number of extensions: 34 Number of successful extensions: 1 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: 552 Length of database: 520 Length adjustment: 35 Effective length of query: 517 Effective length of database: 485 Effective search space: 250745 Effective search space used: 250745 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 (21.7 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