Align Cation acetate symporter (characterized, see rationale)
to candidate RR42_RS06400 RR42_RS06400 acetate permease
Query= uniprot:A0A165ZRB0 (552 letters) >FitnessBrowser__Cup4G11:RR42_RS06400 Length = 546 Score = 709 bits (1830), Expect = 0.0 Identities = 361/533 (67%), Positives = 429/533 (80%), Gaps = 1/533 (0%) Query: 12 AAFAPGAWAAEALTGAVQKQPLNVAAILMFVAFVGATLYITYWASKKNNSAADYYAAGGK 71 AA A A A G+V Q +NV AI MF+ FV ATL +T WA++ N+S AD+YAAGGK Sbjct: 11 AALLLTALPAFAAPGSVG-QGMNVIAIAMFLMFVAATLVVTRWAARSNHSVADHYAAGGK 69 Query: 72 ITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIILFLIAERLRNLG 131 IT QNG AIAGDYMSAAS LGISALVFTSGYDGLIYSIGFL WPIILFLIAE LRNLG Sbjct: 70 ITALQNGWAIAGDYMSAASLLGISALVFTSGYDGLIYSIGFLASWPIILFLIAEPLRNLG 129 Query: 132 KYTFADVASYRLGQTQIRSLSASGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVG 191 ++T ADV SYRL Q IR+ SAS S+V+V YL++QMVGAGKL++LLFG Y AV+LVG Sbjct: 130 RFTLADVVSYRLRQRPIRAFSASSSIVIVLLYLVSQMVGAGKLVELLFGFSYTAAVVLVG 189 Query: 192 ILMCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNMLFAEAVKVHPKGE 251 +LM +YV FGGMLATTW+QIIKAVLLL+GA+FMA MVM F N LFA+A++ H K Sbjct: 190 VLMVVYVFFGGMLATTWIQIIKAVLLLAGAAFMAFMVMSRFGFSLNALFAQAIEAHGKHA 249 Query: 252 AIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVLYATGFIGYFY 311 AIM PGGLV DP+SA SLGLAL+FGTAGLPHILMRFFTV D K ARKS+LYATG +G Y Sbjct: 250 AIMRPGGLVSDPVSAVSLGLALIFGTAGLPHILMRFFTVGDVKAARKSILYATGIVGIGY 309 Query: 312 ILTFIIGFGAILLVSTNPAFKDAAGALLGGNNMAAVHLANAVGGSIFLGFISAVAFATIL 371 L IIGFG I LV+++PA+ AGA++GG NM AVHLA+AVGG++FLGFI AVAF+TIL Sbjct: 310 ALIIIIGFGTIALVASDPAYHTPAGAVIGGVNMVAVHLAHAVGGNLFLGFICAVAFSTIL 369 Query: 372 AVVAGLTLAGASAVSHDLYASVIRKGRVNEKDEIRVSKITTIALAVLAITLGILFEKQNI 431 AVVAGLTLAG+SA+SHDLYA V+R+G +K+E+RVS++TT+ L VL+I LGILFEKQ I Sbjct: 370 AVVAGLTLAGSSAISHDLYAKVLRQGNATDKEEMRVSRMTTLVLGVLSILLGILFEKQTI 429 Query: 432 AFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMIGGWLGLVSAVGLMILGPTIWVQIMG 491 AF+V L FSIAAS NFPVLLLS+YW+ LTTRGA++GG LGL+SAV L +L PT+WVQ++G Sbjct: 430 AFIVSLTFSIAASSNFPVLLLSIYWRGLTTRGAVVGGSLGLLSAVVLTVLSPTVWVQVLG 489 Query: 492 HEKAIFPYEYPALFSMAIAFVGIWFFSITDKSAEGANERALFFPQFVRSQTGL 544 H +AI+PYEYPALFSM +AF GI+ FS+TD+SA GA ER F Q V + GL Sbjct: 490 HARAIYPYEYPALFSMLVAFAGIYVFSVTDRSARGARERGAFNNQLVDCELGL 542 Lambda K H 0.328 0.140 0.414 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: 901 Number of extensions: 48 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: 546 Length adjustment: 36 Effective length of query: 516 Effective length of database: 510 Effective search space: 263160 Effective search space used: 263160 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