Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate 8499545 DvMF_0315 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__Miya:8499545 Length = 519 Score = 575 bits (1481), Expect = e-168 Identities = 301/517 (58%), Positives = 380/517 (73%), Gaps = 14/517 (2%) Query: 32 NWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGLAIAGDYMSAASFLG 91 N +I F +FV FTLG+T+WA++R RS +++Y AG ++TGFQNGLA+AGDYMSAASFLG Sbjct: 13 NALSIGFFFLFVAFTLGVTWWAARRSRSAAEFYAAGRSVTGFQNGLALAGDYMSAASFLG 72 Query: 92 ISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRILSA 151 I+ LV GYDGLIYS+GFLVGWP+++FLIAE LRNLG+YTFADV +YRL+Q PIR+ +A Sbjct: 73 IAGLVALKGYDGLIYSIGFLVGWPVMMFLIAEPLRNLGKYTFADVVAYRLRQRPIRVAAA 132 Query: 152 CGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVVLVGVLMMMYVLFGGMLATTWVQIIK 211 CGSL+ VA YLIAQMVG+G L+ L+FGL Y AV++VG +M+ YVLFGGMLATTWVQIIK Sbjct: 133 CGSLMTVAFYLIAQMVGSGSLVHLMFGLPYETAVLVVGAVMIAYVLFGGMLATTWVQIIK 192 Query: 212 AVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGVDIMKPGGLVKDPISALSLGLGL 271 AVLLL GAS M F V++H GFS LF + A + G ++ PGGLV +P ALSLG+ L Sbjct: 193 AVLLLGGASVMVFFVLRHFGFSPAELFRASAARY--GDKVLAPGGLVSNPWDALSLGMAL 250 Query: 272 MFGTAGLPHILMRFFTVSDAREARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPEYKD 331 MFGTAGLPHILMRF+TV DA+ ARKSVFYATG + YFY+LTFIIGFGA+ LVG ++ Sbjct: 251 MFGTAGLPHILMRFYTVPDAKAARKSVFYATGLISYFYVLTFIIGFGAMTLVG-----QE 305 Query: 332 AAGHLIGGNNMAAVHLANAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANV 391 G NMAA+ LA GG +FLGFI+AVAFATILAVVAGLTLAGA+ +HDLYANV Sbjct: 306 VVAGFDKGGNMAALLLAEVTGGTMFLGFIAAVAFATILAVVAGLTLAGATTYAHDLYANV 365 Query: 392 FKKG-ATEREELRVSKITVLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLS 450 F++G +TE +E+R++K + LGV+A+ LG+ F+ QN+AFMVGLAFAIAAS NFP +L+S Sbjct: 366 FRRGQSTEDDEVRMAKRATVALGVLAVALGIAFKGQNVAFMVGLAFAIAASANFPALLMS 425 Query: 451 MYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQILGHE---KAIFPYEYPALFSITVA 507 + W + +T GA+ G AV L++L PT+WV +L A F + PAL S+ A Sbjct: 426 ILWKRFSTFGAVCSIATGATLAVGLIVLSPTVWVDVLHSPWGMAAPFMLKNPALISLPAA 485 Query: 508 FLGIWFFSATDNSAEGARERELFRAQFIRSQTGFGVE 544 F W S + + + Q IR+ G G E Sbjct: 486 FAAGWLGSVLRPEPDA---EQRYAEQKIRNYLGVGAE 519 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: 867 Number of extensions: 38 Number of successful extensions: 5 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: 519 Length adjustment: 35 Effective length of query: 514 Effective length of database: 484 Effective search space: 248776 Effective search space used: 248776 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