Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_011385106.1 AMB_RS13720 cation acetate symporter
Query= SwissProt::P32705 (549 letters) >NCBI__GCF_000009985.1:WP_011385106.1 Length = 561 Score = 715 bits (1846), Expect = 0.0 Identities = 367/561 (65%), Positives = 440/561 (78%), Gaps = 12/561 (2%) Query: 1 MKRVLTALAATLPF--------AANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYW 52 MK TA+A+ L F AA AA A G E+Q TNW AIIMF+IFV TLGITYW Sbjct: 1 MKTTKTAIASALAFGGTALLASAALAAGADMGGAEKQATNWHAIIMFVIFVGMTLGITYW 60 Query: 53 ASKRVRSRSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLV 112 A+ R ++ +D+Y AGG ITGFQNGLAIAGDYMSAASFLGISALV+ SGYDGLI+S+G+LV Sbjct: 61 AAGRTKTAADFYAAGGGITGFQNGLAIAGDYMSAASFLGISALVYGSGYDGLIFSVGWLV 120 Query: 113 GWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKL 172 GWPIILFLIAERLRNLG+YTFADV YRL + PIR +A GSL+VV YLI QMVGAG+L Sbjct: 121 GWPIILFLIAERLRNLGKYTFADVCGYRLARTPIRTFAATGSLIVVIFYLIGQMVGAGQL 180 Query: 173 IELLFGLNYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGF 232 I+LLFG++Y AV++VG LMM+YV FGGM+ATTWVQIIKA LLL GA+F+AF VM H GF Sbjct: 181 IKLLFGMDYIYAVMIVGALMMVYVTFGGMVATTWVQIIKACLLLGGATFIAFGVMSHFGF 240 Query: 233 SFNNLFSEAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAR 292 SF LF +A+ VHPK V IM PG LV +P+ A+SLG+ LMFGTAGLPHILMRFFTV DAR Sbjct: 241 SFEKLFVKAIEVHPKKVAIMAPGALVTNPVDAISLGMALMFGTAGLPHILMRFFTVPDAR 300 Query: 293 EARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPEYKD---AAGHLIGGNNMAAVHLAN 349 EARKSVFYATGF+GYFYILTFIIGFGAI LV NPEY + L GGNNMAAV LA+ Sbjct: 301 EARKSVFYATGFIGYFYILTFIIGFGAITLVATNPEYLTKGLGSLDLKGGNNMAAVWLAH 360 Query: 350 AVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKIT 408 A+GG+LFLGFISAVAFATILAVV+GLTLAGASA+SHDLYA+V G ATE E+ VSKI Sbjct: 361 AIGGDLFLGFISAVAFATILAVVSGLTLAGASAISHDLYASVIMHGQATEGREVTVSKIA 420 Query: 409 VLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLG 468 + LG+IA++LG++FE QN+AF+V L F++AAS NFP+++LSM+W LTTRGA++GG +G Sbjct: 421 SIGLGIIAVLLGLVFEKQNVAFIVALTFSVAASANFPVLVLSMFWGGLTTRGAVLGGMIG 480 Query: 469 LITAVVLMILGPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERE 528 L+ +V++++L +WVQ G + IFP+ YPALFS+ AF W FS DNS + ER Sbjct: 481 LLMSVIMVVLSKAVWVQSFGFKAEIFPFAYPALFSVPAAFFFSWLFSILDNSPQAQAERA 540 Query: 529 LFRAQFIRSQTGFGVEQGRAH 549 + AQ IRS+TG G E +H Sbjct: 541 AYEAQSIRSETGLGAEGAASH 561 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: 997 Number of extensions: 51 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: 561 Length adjustment: 36 Effective length of query: 513 Effective length of database: 525 Effective search space: 269325 Effective search space used: 269325 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