Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_011385006.1 AMB_RS13215 cation acetate symporter
Query= SwissProt::P32705 (549 letters) >NCBI__GCF_000009985.1:WP_011385006.1 Length = 554 Score = 658 bits (1697), Expect = 0.0 Identities = 328/554 (59%), Positives = 421/554 (75%), Gaps = 5/554 (0%) Query: 1 MKRVLTALAA-TLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRS 59 MKR+L L A +P AA A G E+QP N AI MF FV+ TLGITYWASKR +S Sbjct: 1 MKRILPILLALAVPTAALAGPGDLGGSEKQPINVTAIAMFFAFVMGTLGITYWASKRTKS 60 Query: 60 RSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILF 119 SD+YTAGG ITGFQNGLAIAGDYMSAA+ LG+S++VF +G+DG IY++ F VGWPIILF Sbjct: 61 ASDFYTAGGGITGFQNGLAIAGDYMSAATLLGLSSMVFATGFDGFIYTISFFVGWPIILF 120 Query: 120 LIAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGL 179 L+AERLRNLGRYTFAD+ASYRL Q +R +A GSL VV YLI QMVGAG+LI+LLFGL Sbjct: 121 LLAERLRNLGRYTFADIASYRLDQSKVRTFAAMGSLTVVCFYLIVQMVGAGQLIKLLFGL 180 Query: 180 NYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFS 239 +Y +AV++VGVLM++YV FGGM+ATTWVQIIKA LLL G + + + GFS N+ + Sbjct: 181 DYAVAVIIVGVLMVVYVTFGGMIATTWVQIIKACLLLGGGVLLCALALSKFGFSLENVAA 240 Query: 240 EAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299 +A+ H GV IM PG ++ DP+SA+SL LGL+FGTA LPHILMRFFTV +A+EARKSVF Sbjct: 241 KAVESHKAGVKIMGPGTMLADPVSAVSLSLGLVFGTAALPHILMRFFTVPNAKEARKSVF 300 Query: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKD---AAGHLIGGNNMAAVHLANAVGGNLF 356 A+GF+G+F+++ I+G A+ +VG +P++ + G L+GG NM +HLA A+GG++F Sbjct: 301 VASGFIGFFFLIVCILGLAAVSIVGTDPQFFEGGKVGGKLLGGGNMPVMHLAKALGGDIF 360 Query: 357 LGFISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVI 415 LGF+SAVAFATILAVV+GL LAGASA++HD+YA V +KG ATE EE+RVSK++ L+LGV+ Sbjct: 361 LGFLSAVAFATILAVVSGLALAGASAIAHDIYARVIRKGHATEAEEMRVSKLSSLVLGVV 420 Query: 416 AIILGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVL 475 A+ILG++FE QN+AF+VGL F IAAS NFP++ LSMYW LTT+GA+ GG GL++AV Sbjct: 421 AVILGIMFEKQNVAFLVGLTFGIAASANFPVLFLSMYWRGLTTKGALWGGIAGLVSAVTC 480 Query: 476 MILGPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFI 535 ++L +WV +L + IFPYE+PALFS+T+AFL S D S E+ LF Q++ Sbjct: 481 VVLSKAVWVVVLNNPAPIFPYEHPALFSMTLAFLVTIVVSKLDGSETAKAEKALFDDQYV 540 Query: 536 RSQTGFGVEQGRAH 549 R+QTG G H Sbjct: 541 RAQTGIGAASASNH 554 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: 938 Number of extensions: 47 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: 549 Length of database: 554 Length adjustment: 36 Effective length of query: 513 Effective length of database: 518 Effective search space: 265734 Effective search space used: 265734 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: 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