Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate 18095 b4067 acetate permease (NCBI)
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__Keio:18095 Length = 549 Score = 1069 bits (2765), Expect = 0.0 Identities = 549/549 (100%), Positives = 549/549 (100%) Query: 1 MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60 MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR Sbjct: 1 MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60 Query: 61 SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120 SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL Sbjct: 61 SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120 Query: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN Sbjct: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180 Query: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE Sbjct: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240 Query: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY Sbjct: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300 Query: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI 360 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI Sbjct: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI 360 Query: 361 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKGATEREELRVSKITVLILGVIAIILG 420 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKGATEREELRVSKITVLILGVIAIILG Sbjct: 361 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKGATEREELRVSKITVLILGVIAIILG 420 Query: 421 VLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGP 480 VLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGP Sbjct: 421 VLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGP 480 Query: 481 TIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTG 540 TIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTG Sbjct: 481 TIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTG 540 Query: 541 FGVEQGRAH 549 FGVEQGRAH Sbjct: 541 FGVEQGRAH 549 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: 1181 Number of extensions: 41 Number of successful extensions: 1 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: 549 Length adjustment: 36 Effective length of query: 513 Effective length of database: 513 Effective search space: 263169 Effective search space used: 263169 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