Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate WP_086512000.1 BZY95_RS21865 ABC transporter permease
Query= CharProtDB::CH_088340 (264 letters) >NCBI__GCF_002151265.1:WP_086512000.1 Length = 274 Score = 157 bits (398), Expect = 2e-43 Identities = 79/253 (31%), Positives = 147/253 (58%), Gaps = 3/253 (1%) Query: 10 FMTAIYAYLYIPIIILIVNSFNSSRF-GINWQGFTTKWYSLLMNNDSLLQAAQHSLTMAV 68 F I +L P+++++ SF+S F GF+ +WY + + + + A ++SL +A Sbjct: 21 FCGLILLFLIAPVLVIVPLSFSSGSFLTYPLPGFSLRWYEAIFTSSAWMGALKNSLIVAP 80 Query: 69 FSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLGIQLGF 128 + A + G+L AV L R F GK + +L M+ P +++A+ + F +G+ + Sbjct: 81 LATLLAMIFGTLAAVGLNRAEFPGKGLIVALLISPMVVPLVIVAVGMYFFFAQVGLLNSY 140 Query: 129 WSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMPAVAAG 188 L+ +H +PFVV+TV + L+GFD + A LGA+ + I+LP +P VA+G Sbjct: 141 TGLVLAHTVLGVPFVVITVNATLQGFDFNQVRAGASLGANPMRVFFTIVLPQIVPGVASG 200 Query: 189 WVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSLVMVIAS 248 + +F S D+VVV+ F+ P+ LP++++S ++ +SP + A+ATIL+++S ++++ Sbjct: 201 GLFAFATSFDEVVVALFIASPTERTLPIQMFSGIRENISPAIAAMATILILISTLLLVTM 260 Query: 249 QLIAR--DKTKGN 259 +L+ R ++ KGN Sbjct: 261 ELLRRRSERLKGN 273 Lambda K H 0.329 0.141 0.412 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: 211 Number of extensions: 11 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: 264 Length of database: 274 Length adjustment: 25 Effective length of query: 239 Effective length of database: 249 Effective search space: 59511 Effective search space used: 59511 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: 47 (22.7 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