Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate Dsui_0522 Dsui_0522 SSS sodium solute transporter
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__PS:Dsui_0522 Length = 557 Score = 683 bits (1763), Expect = 0.0 Identities = 341/554 (61%), Positives = 430/554 (77%), Gaps = 3/554 (0%) Query: 2 IRRLLAILGASIFAPAVWAADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNKS 61 + R L +LG + A A +A GE KQPLNV+AI MFV FV +TL ITYWA+ R KS Sbjct: 4 LSRFLPLLGLLLAAGAAYAGPGTVGEAEKQPLNVAAIAMFVAFVLSTLGITYWAANRTKS 63 Query: 62 AADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILF 121 AD+Y AGG ITGFQNGLAIAGDYMSAA+ LG++++V+ GYDG +Y +GF VGWPIILF Sbjct: 64 TADFYTAGGGITGFQNGLAIAGDYMSAATLLGLTSMVFAKGYDGFVYIVGFFVGWPIILF 123 Query: 122 LIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGL 181 L+AERLRNLG++TFAD+ SYRL Q+++R+++A SL VV FYLI QMVGAG+LI+LLFGL Sbjct: 124 LMAERLRNLGRFTFADITSYRLDQSKVRTVAAISSLTVVLFYLITQMVGAGQLIKLLFGL 183 Query: 182 DYHVAVILVGILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALFS 241 DY VAV++VG+LM++YV FGGM+ATTWVQIIKA LLL G + M L+ M H FDF L + Sbjct: 184 DYEVAVVVVGVLMMVYVTFGGMIATTWVQIIKACLLLGGGTLMMLLAMSHFGFDFETLVT 243 Query: 242 EAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVF 301 +A +VH G IM PG L+ DP++A SL L LMFGTAGLPHILMRFFTV DAK+ARKSVF Sbjct: 244 KATEVHKDGTKIMGPGSLLADPVNAVSLSLGLMFGTAGLPHILMRFFTVPDAKQARKSVF 303 Query: 302 YATGFIGYFYILTFIIGFGAILLVSTNPAF---KDAAGALMGGNNMAAVHLANAVGGSIF 358 ATGFIG+F+++ ++G AI+LV TNP F + G ++GG NM A+HLA VGG+IF Sbjct: 304 VATGFIGFFFLVVVLLGMSAIVLVGTNPEFFEGGNVGGKMIGGGNMVAMHLAKFVGGNIF 363 Query: 359 LGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVL 418 LGF+SAVAFATILAVV+GL LAGASA+SHD+YA+VI KGK E++VSKI +I +G+ Sbjct: 364 LGFLSAVAFATILAVVSGLALAGASAISHDIYANVICKGKPKGGSELKVSKIASIFIGLA 423 Query: 419 AIGLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGL 478 AIGLGI+FE QN+AFMVGLAF IAAS NFPVL+LSMYWK LTT+GA+ G GL +AV Sbjct: 424 AIGLGIMFEKQNLAFMVGLAFGIAASANFPVLILSMYWKGLTTKGAIAGTICGLTAAVVF 483 Query: 479 MVLGPTIWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFV 538 +VL +WV++L +AIFPY+ PALFSM +AF+ + S D S+ A++E + Q+V Sbjct: 484 VVLSKAVWVTVLGKAQAIFPYDQPALFSMPLAFLIAFVVSKLDTSAQAKREIEAFDDQYV 543 Query: 539 RSQTGLGSSGAVSH 552 R+QTGLG++GA +H Sbjct: 544 RAQTGLGAAGASNH 557 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: 957 Number of extensions: 37 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: 552 Length of database: 557 Length adjustment: 36 Effective length of query: 516 Effective length of database: 521 Effective search space: 268836 Effective search space used: 268836 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: 53 (25.0 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