Align putrescine transport system permease protein PotH (characterized)
to candidate GFF5026 PS417_25750 polyamine ABC transporter substrate-binding protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__WCS417:GFF5026 Length = 415 Score = 162 bits (411), Expect = 1e-44 Identities = 79/219 (36%), Positives = 138/219 (63%), Gaps = 4/219 (1%) Query: 91 DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIR 150 D +Y D + ++ + + T CLL+ YPLA+ +A+ N+L++LV+LP WTS L+R Sbjct: 189 DQAIYLDIFARTFWMGLVITAVCLLLAYPLAYLLANLPARQSNLLMILVLLPFWTSILVR 248 Query: 151 VYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRI 210 V AW+ +L++ G++N+ L+ +G+ID+PL ++ VYI +V+ +PFM+LPIY+ + I Sbjct: 249 VAAWIVLLQSGGLINSALMGMGLIDKPLELVFNRTGVYISMVHILLPFMILPIYSVMKGI 308 Query: 211 DYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMI 270 + + AA+ LG P +F+ V P T G+ AG +LVFI A+G ++ P LLG P+ M+ Sbjct: 309 SPTYMRAAISLGCHPFTSFWRVYFPQTYAGVGAGCLLVFILAIGYYITPALLGSPNDQMV 368 Query: 271 GRVLWQEFFNNR--DWPVASAVAIIMLLLLIVPIMWFHK 307 + F+ N +W +A+A+ ++LL +V + +++ Sbjct: 369 S--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: 329 Number of extensions: 14 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