Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate CCNA_03236 CCNA_03236 spermidine/putrescine transport system permease protein potC
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__Caulo:CCNA_03236 Length = 291 Score = 199 bits (507), Expect = 4e-56 Identities = 100/246 (40%), Positives = 161/246 (65%), Gaps = 7/246 (2%) Query: 10 FMTAIYAYLYIPIIILIVNSFNSSRFGINWQGFTTKWYSLLMNNDSLLQAAQHSLTMAVF 69 ++ A++ +LY P+I L+ SFN S+ I W+GFT K+Y L NN LL+A +SLT+A Sbjct: 27 WLAAVFIFLYAPLIALMAFSFNDSKRNIVWKGFTLKYYEKLFNNSELLEAFGNSLTIAAA 86 Query: 70 SATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLL-----GI 124 S + +G+ A+AL+R+RF GK V G + + ++ P+I M +++LV F + G+ Sbjct: 87 STVISLFLGAAVALALWRFRFPGKTAVDGAMALPIVVPEICMGVAMLVFFAKVLPWPQGM 146 Query: 125 Q--LGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAM 182 L +++ +H++F PFV V V +R+ F+ M EAA+DLGA EF ++ +ILP Sbjct: 147 PWPLNLGAIIIAHVSFSFPFVAVVVRARMASFNREMEEAARDLGAGEFRTIKDVILPHMA 206 Query: 183 PAVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSL 242 P++ AG +L+FTLS+DD V++ F GP P+K+YSMV+ V+PEVNA +T+L+VL++ Sbjct: 207 PSLIAGALLAFTLSLDDFVITFFTAGPDTVTFPVKVYSMVRFSVTPEVNAASTVLIVLTV 266 Query: 243 VMVIAS 248 ++ A+ Sbjct: 267 LLTAAA 272 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: 197 Number of extensions: 9 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: 291 Length adjustment: 25 Effective length of query: 239 Effective length of database: 266 Effective search space: 63574 Effective search space used: 63574 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