Align putrescine transport system permease protein PotH (characterized)
to candidate AO356_14395 AO356_14395 polyamine ABC transporter substrate-binding protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_14395 Length = 415 Score = 162 bits (409), Expect = 2e-44 Identities = 81/229 (35%), Positives = 142/229 (62%), Gaps = 5/229 (2%) Query: 82 NLGNFLQLT-DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVI 140 +LG T D +Y D + ++ + + T CL++ YPLA+ +A+ N+L++LV+ Sbjct: 179 DLGELAPATPDQAIYLDIFTRTFWMGLVITAICLVLAYPLAYLLANLPSRQSNLLMILVL 238 Query: 141 LPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMV 200 LP WTS L+RV AW+ +L++ G++N+ L+ +G+ID+PL ++ VYI +V+ +PFM+ Sbjct: 239 LPFWTSILVRVAAWIVLLQSGGLINSGLMAMGIIDKPLELVFNRTGVYISMVHILLPFMI 298 Query: 201 LPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPE 260 LPIY+ + I + + AA+ LG P +F+ V P T G+ AG +LVFI A+G ++ P Sbjct: 299 LPIYSVMKGISPTYMRAAISLGCHPFASFWRVYFPQTYAGVGAGCLLVFILAIGYYITPA 358 Query: 261 LLGGPDSIMIGRVLWQEFFNNR--DWPVASAVAIIMLLLLIVPIMWFHK 307 LLG P+ M+ + F+ N +W +A+A+ ++LL +V + +++ Sbjct: 359 LLGSPNDQMVS--YFVAFYTNTSINWGMATALGGLLLLATVVLYLIYNR 405 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: 333 Number of extensions: 17 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: 317 Length of database: 415 Length adjustment: 29 Effective length of query: 288 Effective length of database: 386 Effective search space: 111168 Effective search space used: 111168 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: 49 (23.5 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