Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate Pf6N2E2_4818 Spermidine Putrescine ABC transporter permease component potC (TC_3.A.1.11.1)
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4818 Length = 269 Score = 150 bits (380), Expect = 2e-41 Identities = 77/234 (32%), Positives = 139/234 (59%), Gaps = 1/234 (0%) Query: 14 IYAYLYIPIIILIVNSFNSSRFGIN-WQGFTTKWYSLLMNNDSLLQAAQHSLTMAVFSAT 72 I +L +P++++I SFNS F + QGF+ +WY + ++A ++S+ +A + Sbjct: 19 ILLFLILPVLVIIPLSFNSGSFLVYPLQGFSLQWYHDFFASAEWMRALKNSIIVAPAATL 78 Query: 73 FATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLGIQLGFWSLL 132 A + G+L A+ L R F GK V ++ M+ P +++ ++ + F LG+ F+SL+ Sbjct: 79 LAMVFGTLAAIGLTRGDFPGKALVMALVISPMVVPVVIIGVASYLFFAPLGMGNSFFSLI 138 Query: 133 FSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMPAVAAGWVLS 192 H +PFV++TV + L+GF+ ++ AA LGAS T R++ LPL P V +G + + Sbjct: 139 VVHAVLGVPFVIITVSATLQGFNHNLVRAAASLGASPLTAFRRVTLPLIAPGVISGALFA 198 Query: 193 FTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSLVMVI 246 F S D+VVV+ F+ GP LP +++S ++ +SP + A AT+L+ S+++++ Sbjct: 199 FATSFDEVVVTLFLAGPEQATLPRQMFSGIRENLSPTIAAAATLLIAFSVILLL 252 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: 194 Number of extensions: 7 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: 269 Length adjustment: 25 Effective length of query: 239 Effective length of database: 244 Effective search space: 58316 Effective search space used: 58316 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 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