Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate HSERO_RS05400 HSERO_RS05400 polyamine ABC transporter permease
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__HerbieS:HSERO_RS05400 Length = 277 Score = 152 bits (383), Expect = 1e-41 Identities = 79/240 (32%), Positives = 141/240 (58%), Gaps = 1/240 (0%) Query: 9 GFMTAIYAYLYIPIIILIVNSFNSSRFGIN-WQGFTTKWYSLLMNNDSLLQAAQHSLTMA 67 GF + +L PI+++I SF+ S F + + F+ +WY L ++D ++AAQ+S +A Sbjct: 24 GFNLLVLLFLVSPILVMIPLSFSDSSFLMYPIKSFSLRWYENLFSSDDWVRAAQNSFIVA 83 Query: 68 VFSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLGIQLG 127 + AT++G+L AV L + FRGK + +L M+ P +V+ + + + F +G+ Sbjct: 84 PAATVIATVLGTLAAVGLNKADFRGKGILMAILISPMIVPVVVVGVGVYLFFARIGLSDS 143 Query: 128 FWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMPAVAA 187 + L+ +H PFVV TV + L+GF+ ++ A+ LGAS ++ LP+ P + + Sbjct: 144 YLGLILAHAALGAPFVVTTVLATLQGFNHNLVRASLSLGASPLRTFFRVTLPVIAPGLIS 203 Query: 188 GWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSLVMVIA 247 G + +F S D+VV++ FV GP LP ++++ +K +SP + ALATIL++ S +++A Sbjct: 204 GALFAFATSFDEVVLTLFVAGPEQATLPRQMFAGIKDNISPTIAALATILIIFSTCLLLA 263 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: 188 Number of extensions: 9 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: 277 Length adjustment: 25 Effective length of query: 239 Effective length of database: 252 Effective search space: 60228 Effective search space used: 60228 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