Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate 209382 DVU0446 sodium/solute symporter family protein
Query= SwissProt::P32705 (549 letters) >MicrobesOnline__882:209382 Length = 515 Score = 570 bits (1470), Expect = e-167 Identities = 310/515 (60%), Positives = 375/515 (72%), Gaps = 13/515 (2%) Query: 32 NWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGLAIAGDYMSAASFLG 91 N +I+ F FV FTL IT++A++R RS S++Y AG ++TG QNGLA+AGDYMSAASFLG Sbjct: 12 NAVSILFFFAFVAFTLAITWFAARRSRSASEFYAAGRSVTGLQNGLALAGDYMSAASFLG 71 Query: 92 ISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRILSA 151 I+ LV GYDGLIYS+GFLVGWP+++FLIAE LRNLGRYTFADV +YRL+Q PIRI +A Sbjct: 72 IAGLVSLKGYDGLIYSIGFLVGWPLMMFLIAEPLRNLGRYTFADVVAYRLRQKPIRIAAA 131 Query: 152 CGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVVLVGVLMMMYVLFGGMLATTWVQIIK 211 CGSL+ V YLIAQMVG+G L++L+FG+ Y AVV VG +MM YVLFGGMLATTWVQI K Sbjct: 132 CGSLMTVCFYLIAQMVGSGALVQLMFGIRYEYAVVAVGFIMMAYVLFGGMLATTWVQITK 191 Query: 212 AVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGVDIMKPGGLVKDPISALSLGLGL 271 AVLLL GA+ M MV+ +S LF A A H G ++ PGGLV +P A+SLG+ L Sbjct: 192 AVLLLGGATAMVVMVLAQFDYSPTRLFVTAAAKH--GEAMLAPGGLVSNPWDAISLGMAL 249 Query: 272 MFGTAGLPHILMRFFTVSDAREARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPEYKD 331 MFGTAGLPHILMRF+TV DAR ARKSVFYATG + YFY+LTFIIGFGA+MLVG D Sbjct: 250 MFGTAGLPHILMRFYTVPDARAARKSVFYATGLISYFYVLTFIIGFGAMMLVG-----PD 304 Query: 332 AAGHLIGGNNMAAVHLANAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANV 391 A G NMAA LA GG +FLGFI+AVAFATILAVVAGLTLAGA+ SHDLYANV Sbjct: 305 AIRMFDKGGNMAAPLLAEVTGGTMFLGFIAAVAFATILAVVAGLTLAGATTFSHDLYANV 364 Query: 392 FKKG-ATEREELRVSKITVLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLS 450 FK G + E +E+RV+K + LGVIA++LG+ F+ QN+AFMVGLAFAIAAS N P +LLS Sbjct: 365 FKGGQSNEADEVRVAKRATIALGVIAMLLGIAFKGQNVAFMVGLAFAIAASANLPALLLS 424 Query: 451 MYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQILGHEKAIFPYEYPALFSITVAFL- 509 + W +T GA+ G + AV L+I+ PT+W + A FP + PAL S+ AF+ Sbjct: 425 IMWRGCSTTGAVWAIVTGGVLAVGLIIVSPTVWTDVFHLGTAPFPLKNPALLSMPAAFMA 484 Query: 510 GIWFFSATDNSAEGARERELFRAQFIRSQTGFGVE 544 GI +S E AR F AQ IR+ G G E Sbjct: 485 GIAGSLLRPDSEESAR----FDAQKIRNYLGVGAE 515 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: 825 Number of extensions: 41 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: 515 Length adjustment: 35 Effective length of query: 514 Effective length of database: 480 Effective search space: 246720 Effective search space used: 246720 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