Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate PfGW456L13_1568 Spermidine Putrescine ABC transporter permease component PotB (TC 3.A.1.11.1)
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1568 Length = 306 Score = 208 bits (529), Expect = 1e-58 Identities = 107/262 (40%), Positives = 166/262 (63%), Gaps = 11/262 (4%) Query: 11 LFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLL------DPL-----YFEVLLHSL 59 LF+ +P L++IG S + + V VF+ D YT LL D L Y + L S+ Sbjct: 31 LFLIVPILIVIGYSLMEANPYGGVNKVFSSDAYTSLLFERQLDDSLAFADSYLIIALRSI 90 Query: 60 NMALIATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGY 119 +A + TL L++G+P A +LA P R LL+FL+ VPFW N LIR Y + L G Sbjct: 91 GIAGLTTLITLLIGFPVAVWLAMQPAHRRGLLIFLITVPFWANLLIRTYAWILLLRNTGV 150 Query: 120 LNEFLLWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGA 179 +N L+ LGVID P+++++T AV++G+VY PF+V+P+Y+++EK+D LLEAA+DL A Sbjct: 151 INNSLMGLGVIDQPLQLLYTDGAVLLGVVYTYAPFVVLPIYATLEKMDIRLLEAAQDLYA 210 Query: 180 SKLQTFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRD 239 +++T ++++P+ PGI+AG +L +P +G +L+GG +++GN+I QF + R+ Sbjct: 211 GRVRTLRKVVLPIAKPGILAGAILTFVPCLGAMIAPELLGGGTRMMLGNLIFRQFSDARN 270 Query: 240 WPFGAATSITLTIVMGLMLLVY 261 WPFGAA S+ L + L+L VY Sbjct: 271 WPFGAALSLVLMAAVMLVLTVY 292 Lambda K H 0.333 0.148 0.456 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: 282 Number of extensions: 11 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: 275 Length of database: 306 Length adjustment: 26 Effective length of query: 249 Effective length of database: 280 Effective search space: 69720 Effective search space used: 69720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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