Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate AZOBR_RS01220 AZOBR_RS01220 ABC transporter permease
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__azobra:AZOBR_RS01220 Length = 294 Score = 163 bits (413), Expect = 4e-45 Identities = 95/272 (34%), Positives = 155/272 (56%), Gaps = 5/272 (1%) Query: 1 MIVTIVGWLVLFVFLPNLMIIGTSF---LTRDDASFVKMVFTLDNYTRL-LDPLYFEVLL 56 +++ + WL+L V LP L+++ SF L A + V+TL NY L + ++ + L Sbjct: 16 ILLAVAVWLLLLVVLPQLLMVDFSFRPSLPPSKAGGPEDVYTLRNYATLWTNQIHLAIFL 75 Query: 57 HSLNMALIATLACLVLGYPFAWFLAKLPHKVR-PLLLFLLIVPFWTNSLIRIYGLKIFLS 115 ++ + + T L + YP A+++A++ + R PLL+ +L+VPFW N L+R + I L+ Sbjct: 76 KTIWASSLVTAVTLAVCYPVAFYMAQVASRRRLPLLVLMLVVPFWINELLRTFAWYIILA 135 Query: 116 TKGYLNEFLLWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAAR 175 G LN L+ LG+ P R++ + VIIG+VY+ + FMV P+ +++E LD+ +EAAR Sbjct: 136 FNGPLNALLVGLGLFSEPQRLLGGDAGVIIGMVYVYILFMVFPIMNAMESLDRNQIEAAR 195 Query: 176 DLGASKLQTFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFL 235 DLGA L+ RI+IP PGI GC++ + A G + V L+GG ++ VI F Sbjct: 196 DLGAGWLRIHRRIVIPHAKPGIAVGCIMTFMLAAGSYAVPALLGGPQSRWFTEVIYNWFF 255 Query: 236 NIRDWPFGAATSITLTIVMGLMLLVYWRASRL 267 +W GAA + L I+ +L+ R R+ Sbjct: 256 EGGNWNQGAAYAFILLILCVAFILLMMRLFRV 287 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: 253 Number of extensions: 17 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: 294 Length adjustment: 26 Effective length of query: 249 Effective length of database: 268 Effective search space: 66732 Effective search space used: 66732 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: 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