Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate WP_003473551.1 J416_RS13350 cation acetate symporter
Query= TCDB::D5APM1 (578 letters) >NCBI__GCF_000359605.1:WP_003473551.1 Length = 560 Score = 195 bits (495), Expect = 5e-54 Identities = 142/480 (29%), Positives = 230/480 (47%), Gaps = 52/480 (10%) Query: 63 RTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLVGWP 122 R + ++FY AG G+ NG AIA D+MSAASF+ ++ V GYDG IY +G+ G+ Sbjct: 26 RVRDTSNFYVAGQGVPTVANGAAIAADWMSAASFISMAGLVAFLGYDGTIYLMGWTGGYV 85 Query: 123 ILTFLMAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQLIKL 182 +L L+A LR GKFT D F + R AA++T+ + Y+ QM G G + Sbjct: 86 LLALLLAPYLRKFGKFTVPDFIGDRFYSSTARSVAAIATIFISLTYISGQMRGVGIVFSR 145 Query: 183 LFGLEYLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGFSLE 242 ++ + V++ ++ + L GGM TW Q I+ +++ A + F L Sbjct: 146 YLQVDIIIGVLIGMAIVGFFALLGGMKGVTWTQAIQYFVIIIAFLIPAFAI----SFQLT 201 Query: 243 SLFADSVKVKT-DLALAAGKTPEEAAAAGISIMGPGTFVKDPISAISFGMALMFGTAGLP 301 + + T D+ G+ E M P T + ++ + +ALM GTAGLP Sbjct: 202 GNPIPQLALTTSDIVDRLGQIQVELGMT--EYMAPFTDL-SMLNVLMMTLALMAGTAGLP 258 Query: 302 HILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIG----FGAIVYVLTNP-------- 349 H+++RF+TV S + AR S +WA V+IG Y+ +G + I + P Sbjct: 259 HVIVRFYTVKSVRAARWSAVWAIVFIGLLYVTAPAVGAFAKYNLIDTIADKPIEEVQDID 318 Query: 350 GLVSYDAKGALTLVGGNNMAAIHLA------QAVGGNI--------------FLGFISAV 389 + ++ G L L N ++ + G+I + ++A Sbjct: 319 WVNKWETTGLLQLDDANGDGIVNFTGDDQNEVMIDGDIIVLSTPEVANLAPFIIALVAAG 378 Query: 390 AFATILAVVAGLTLSGASAVSHDLYSTVFKNGKADSASELRVSRITTICLGIVAVVLGL- 448 A L+ +GL ++ SAVSHD+Y +F N KA A LRV RIT ++A +G+ Sbjct: 379 GLAAALSTASGLLITMTSAVSHDIYYRIF-NKKASEAQRLRVGRITLFVALLIAAYVGIN 437 Query: 449 --AFEKQNIAFMVSLAFAIAASANFPVLFMSLLWKGMTTRGAVIGGSLGLISSVALTVIS 506 F + +V+LAF + A++ FPV+ + + K M GAV G+I+ ++ T+I+ Sbjct: 438 PPGFAGE----VVALAFGLGAASLFPVILLGIFDKRMNKEGAV----AGIITGLSFTLIT 489 Lambda K H 0.326 0.138 0.405 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: 898 Number of extensions: 53 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: 578 Length of database: 560 Length adjustment: 36 Effective length of query: 542 Effective length of database: 524 Effective search space: 284008 Effective search space used: 284008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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