Align putrescine transport system permease protein PotH (characterized)
to candidate AO356_25725 AO356_25725 ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25725 Length = 309 Score = 161 bits (408), Expect = 2e-44 Identities = 84/238 (35%), Positives = 138/238 (57%) Query: 75 GQLSITLNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNI 134 G L LGN+ QL + Y + VA + T LL+G+PLAWA+ Sbjct: 64 GVLEPVPGLGNYEQLFANSAYARVLFNTFSVAGLVTLFSLLLGFPLAWAITLVPRGWGRW 123 Query: 135 LLLLVILPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYA 194 +L +V+L WTS L R Y+W+ +L+ +GV+N L+ LG+IDQPL ++H V IG+ Y Sbjct: 124 MLNIVLLSMWTSLLARTYSWLVLLQASGVVNKALMALGIIDQPLEMVHNLTGVVIGMSYI 183 Query: 195 YVPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVG 254 +PF+VLP+ + ID +++A GA P FF V +PL + G+ +G ++VF+ ++G Sbjct: 184 MIPFIVLPLQATMQAIDPMILQAGSICGASPWTNFFRVFLPLCRPGLFSGGLMVFVMSLG 243 Query: 255 EFVIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKS 312 +V P LLGG ++M+ + Q+ + +W +ASA A +++ + +V ++ K Q +S Sbjct: 244 YYVTPALLGGAQNMMLPEFIIQQVQSFLNWGLASAGAALLVAITLVLFYFYLKLQPES 301 Lambda K H 0.328 0.144 0.457 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: 260 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 317 Length of database: 309 Length adjustment: 27 Effective length of query: 290 Effective length of database: 282 Effective search space: 81780 Effective search space used: 81780 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 (21.7 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