Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate PP_1743 PP_1743 acetate permease
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__Putida:PP_1743 Length = 554 Score = 851 bits (2199), Expect = 0.0 Identities = 430/533 (80%), Positives = 473/533 (88%), Gaps = 1/533 (0%) Query: 18 AADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGL 77 AADA++G V++QP N AI MF+ FV FTLGITYWASKR +S SDYY AGG ITGFQNGL Sbjct: 22 AADALTGEVQKQPLNVSAIAMFVAFVAFTLGITYWASKRNKSASDYYAAGGKITGFQNGL 81 Query: 78 AIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVA 137 AIAGDYMSAASFLGISALVFTSGYDGLIYS+GFLVGWPIILFLIAERLRNLG+YTFADVA Sbjct: 82 AIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVA 141 Query: 138 SYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVVLVGVLMMMYVL 197 SYRL Q IR LSA GSLVVVA YLIAQMVGAGKLIELLFGL+YH+AV+LVG+LM +YVL Sbjct: 142 SYRLGQKEIRTLSASGSLVVVAFYLIAQMVGAGKLIELLFGLDYHVAVILVGILMCLYVL 201 Query: 198 FGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGVDIMKPGGL 257 FGGMLATTWVQIIKAVLLL GASFMA MVMKHVGF FN LFSEA+ VH KG IM PGGL Sbjct: 202 FGGMLATTWVQIIKAVLLLSGASFMALMVMKHVGFDFNTLFSEAIKVHAKGEAIMSPGGL 261 Query: 258 VKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGFMGYFYILTFIIGF 317 VKDPISA SLGL LMFGTAGLPHILMRFFTVSDA+EARKSV YATGF+GYFYILTFIIGF Sbjct: 262 VKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVLYATGFIGYFYILTFIIGF 321 Query: 318 GAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFISAVAFATILAVVAGLTL 377 GAI+LV NPE+KDAAG L+GGNNMAAVHLANAVGG++FLGFISAVAFATILAVVAGLTL Sbjct: 322 GAILLVSTNPEFKDAAGALLGGNNMAAVHLANAVGGSVFLGFISAVAFATILAVVAGLTL 381 Query: 378 AGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIILGVLFENQNIAFMVGLAF 436 AGASAVSHDLYA+V++KG A +++E+RVSKIT + LGV+AI LG+LFE QNIAFMVGLAF Sbjct: 382 AGASAVSHDLYASVWRKGKANDKDEIRVSKITTVALGVLAIGLGILFEKQNIAFMVGLAF 441 Query: 437 AIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQILGHEKAIFPY 496 +IAASCNFP++LLSMYW KLTTRGAM+GGWLGL++AV LMILGPTIWVQILGHEK I+PY Sbjct: 442 SIAASCNFPVLLLSMYWKKLTTRGAMIGGWLGLVSAVTLMILGPTIWVQILGHEKPIYPY 501 Query: 497 EYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTGFGVEQGRAH 549 EYPALFS+ +AF+ IWFFS TD S ER LF QF+RSQTG G +H Sbjct: 502 EYPALFSMAIAFVSIWFFSVTDKSKAAEDERALFFPQFVRSQTGLGASGAVSH 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: 1033 Number of extensions: 44 Number of successful extensions: 2 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