Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate 3608193 Dshi_1598 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__Dino:3608193 Length = 268 Score = 159 bits (401), Expect = 8e-44 Identities = 82/239 (34%), Positives = 141/239 (58%), Gaps = 3/239 (1%) Query: 17 YLYIPIIILIVNSFNSSRF-GINWQGFTTKWYSLLMNNDSLLQAAQHSLTMAVFSATFAT 75 +LY+P+ +L + +FN S GFT W+ L +L A ++SL +A+ +A F+T Sbjct: 16 FLYLPVALLPIFAFNDSTIIAFPLSGFTISWFVELTQIPALHDAVRNSLIIALSTAVFST 75 Query: 76 LIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLGIQLGFWSLLFSH 135 +G + A R+ F GK + G + + ++ P+I++A+SLLV+ + +G+ L W+++ H Sbjct: 76 ALGVFASRAATRFEFPGKAGIMGFIMIPLVLPEIIVAVSLLVVLLQMGLNLSLWAVILGH 135 Query: 136 ITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMPAVAAGWVLSFTL 195 C PF + + S G D + EAA DLG + + R IILPL P + A ++SFT+ Sbjct: 136 TLICTPFCIAILSSSFSGLDRSLEEAAIDLGETRLSAFRLIILPLVAPGIVASLLISFTI 195 Query: 196 SMDDVVVSSFVTGPSYEILPLKIYSMVKVGVS-PEVNALATILLVLSLVMVIASQLIAR 253 S+D+ +++ F+TG LP+ I+S ++ P + AL TIL++LSLV++I ++ R Sbjct: 196 SLDEFIIAFFLTGTD-PTLPVYIWSQLRFPQKLPVIMALGTILILLSLVLIITAEAFRR 253 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: 192 Number of extensions: 10 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: 264 Length of database: 268 Length adjustment: 25 Effective length of query: 239 Effective length of database: 243 Effective search space: 58077 Effective search space used: 58077 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