Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate 8499545 DvMF_0315 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__Miya:8499545 Length = 519 Score = 587 bits (1514), Expect = e-172 Identities = 306/516 (59%), Positives = 382/516 (74%), Gaps = 13/516 (2%) Query: 34 NVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGKITGFQNGLAIAGDYMSAASFLG 93 N +I F +FV TL +T+WA++R++SAA++YAAG +TGFQNGLA+AGDYMSAASFLG Sbjct: 13 NALSIGFFFLFVAFTLGVTWWAARRSRSAAEFYAAGRSVTGFQNGLALAGDYMSAASFLG 72 Query: 94 ISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVASYRLGQTQIRSLSA 153 I+ LV GYDGLIYSIGFLVGWP+++FLIAE LRNLGKYTFADV +YRL Q IR +A Sbjct: 73 IAGLVALKGYDGLIYSIGFLVGWPVMMFLIAEPLRNLGKYTFADVVAYRLRQRPIRVAAA 132 Query: 154 CGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVGILMVLYVLFGGMLATTWVQIIK 213 CGSL+ VAFYLIAQMVG+G L+ L+FGL Y AV++VG +M+ YVLFGGMLATTWVQIIK Sbjct: 133 CGSLMTVAFYLIAQMVGSGSLVHLMFGLPYETAVLVVGAVMIAYVLFGGMLATTWVQIIK 192 Query: 214 AVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGEAIMSPGGLVKDPISAFSLGLAL 273 AVLLL GAS M V++H F LF + + G+ +++PGGLV +P A SLG+AL Sbjct: 193 AVLLLGGASVMVFFVLRHFGFSPAELFRASAARY--GDKVLAPGGLVSNPWDALSLGMAL 250 Query: 274 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAILLVSTNPAFKD 333 MFGTAGLPHILMRF+TV DAK ARKSVFYATG I YFY+LTFIIGFGA+ LV ++ Sbjct: 251 MFGTAGLPHILMRFYTVPDAKAARKSVFYATGLISYFYVLTFIIGFGAMTLVG-----QE 305 Query: 334 AAGALMGGNNMAAVHLANAVGGSIFLGFISAVAFATILAVVAGLTLAGASAVSHDLYASV 393 G NMAA+ LA GG++FLGFI+AVAFATILAVVAGLTLAGA+ +HDLYA+V Sbjct: 306 VVAGFDKGGNMAALLLAEVTGGTMFLGFIAAVAFATILAVVAGLTLAGATTYAHDLYANV 365 Query: 394 IKKGKANDKDEIRVSKITTIALGVLAIGLGILFESQNIAFMVGLAFSIAASCNFPVLLLS 453 ++G++ + DE+R++K T+ALGVLA+ LGI F+ QN+AFMVGLAF+IAAS NFP LL+S Sbjct: 366 FRRGQSTEDDEVRMAKRATVALGVLAVALGIAFKGQNVAFMVGLAFAIAASANFPALLMS 425 Query: 454 MYWKNLTTRGAMIGGWLGLVSAVGLMVLGPTIWVSILHHE---KAIFPYEYPALFSMIIA 510 + WK +T GA+ G AVGL+VL PT+WV +LH A F + PAL S+ A Sbjct: 426 ILWKRFSTFGAVCSIATGATLAVGLIVLSPTVWVDVLHSPWGMAAPFMLKNPALISLPAA 485 Query: 511 FVGIWFFSITDKSSAAEKERALYFPQFVRSQTGLGS 546 F W S+ AE+ Y Q +R+ G+G+ Sbjct: 486 FAAGWLGSVLRPEPDAEQR---YAEQKIRNYLGVGA 518 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: 883 Number of extensions: 46 Number of successful extensions: 3 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: 519 Length adjustment: 35 Effective length of query: 517 Effective length of database: 484 Effective search space: 250228 Effective search space used: 250228 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