Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter
Query= SwissProt::P32705 (549 letters) >NCBI__GCF_000009985.1:WP_011386681.1 Length = 554 Score = 668 bits (1723), Expect = 0.0 Identities = 346/546 (63%), Positives = 418/546 (76%), Gaps = 4/546 (0%) Query: 5 LTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYY 64 L LA +LP A AD G RQ TNW AI+MF+ FV+ TLGIT+WASKR +S +D+Y Sbjct: 12 LMLLAPSLPALAAGADL--GQAARQATNWHAILMFVGFVLLTLGITWWASKRTKSAADFY 69 Query: 65 TAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAER 124 TAGG ITGFQNGLAIAGD+MSAASFLG++AL++ +G DG++Y++G +VGWP++LFLIAE Sbjct: 70 TAGGGITGFQNGLAIAGDFMSAASFLGVTALLYGTGLDGMVYAVGVVVGWPLMLFLIAEP 129 Query: 125 LRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIA 184 LRNLG+YTFADV +YRL + P+R +A SL VV YLIAQMVGAG+LI+LLFG++Y A Sbjct: 130 LRNLGKYTFADVVAYRLAKVPVRTYAAFSSLTVVVFYLIAQMVGAGQLIKLLFGMDYLYA 189 Query: 185 VVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAV 244 + LVG LMM+YV FGGM ATTWVQIIKAVLLL GA+FMA V+ GFS +F++A+ V Sbjct: 190 LFLVGGLMMIYVTFGGMAATTWVQIIKAVLLLSGATFMAGAVLSRFGFSPEAMFAKAVQV 249 Query: 245 HPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGF 304 IM PG L KDPI +SL + L FGTAGLPHILMRFFTV DA+EARKSVFYAT F Sbjct: 250 KGSNA-IMSPGLLFKDPIDTISLAMALAFGTAGLPHILMRFFTVPDAKEARKSVFYATAF 308 Query: 305 MGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFISAVA 364 +G+FY+L +IG GAI LV +P Y L GG NMAAV LA+AVGG+LFLGFISAVA Sbjct: 309 IGFFYVLAVVIGIGAIALVATDPTYLADGKALKGGGNMAAVWLAHAVGGDLFLGFISAVA 368 Query: 365 FATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIILGVLF 423 FATILAVVAGLTLAGASA+SHDLYANVF +G A E ELR+S++ L LGVIAIILG+LF Sbjct: 369 FATILAVVAGLTLAGASAISHDLYANVFARGHAKEETELRISRLASLALGVIAIILGMLF 428 Query: 424 ENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGPTIW 483 E QNIA++ GL AIAAS NFP++LLSM W LT+RGA++GG GL++AVVL +LGP +W Sbjct: 429 EKQNIAYLAGLTLAIAASANFPLLLLSMLWPGLTSRGAILGGVAGLVSAVVLTVLGPAVW 488 Query: 484 VQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTGFGV 543 +LG+ + IFP+ PALFS+ F WFFS TD S RE+ F AQF+RSQTG G Sbjct: 489 KAVLGNPQPIFPWGNPALFSVAAGFAATWFFSVTDGSERAVREKAEFNAQFVRSQTGLGA 548 Query: 544 EQGRAH 549 E AH Sbjct: 549 EGVSAH 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: 950 Number of extensions: 46 Number of successful extensions: 4 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