Align putrescine transport system permease protein PotH (characterized)
to candidate HSERO_RS05405 HSERO_RS05405 polyamine ABC transporter substrate-binding protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__HerbieS:HSERO_RS05405 Length = 427 Score = 145 bits (365), Expect = 2e-39 Identities = 73/224 (32%), Positives = 131/224 (58%) Query: 91 DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIR 150 + +Y + ++L ++A+ T LL+ YPLA+ ++ N+L++LV++P WTS L+R Sbjct: 202 ESAIYRTIFGRTLWMSAVVTCITLLLAYPLAYWLSTMPERRANLLMILVLIPFWTSILVR 261 Query: 151 VYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRI 210 V AW+ +L++ G++N L+ G+ PL ++ + VYI + + +PFM+LP+Y+ + + Sbjct: 262 VAAWIVLLQSEGLVNKALMLAGLTQSPLELVFNRVGVYISMTHILLPFMILPLYSVMKSV 321 Query: 211 DYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMI 270 + ++AA+ LG+ P F+ V VP T GI AG +LVFI A G ++ P LLGGP+ M+ Sbjct: 322 PATYLKAAVSLGSHPFAAFWRVYVPQTYPGIGAGVLLVFIMAGGYYITPALLGGPNEQMV 381 Query: 271 GRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSVG 314 + +W +A A+ ++L +V + + + VG Sbjct: 382 SYFIAYFINTTINWGMACALGALLLAATLVLYGVYRRFAKVDVG 425 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: 318 Number of extensions: 25 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: 427 Length adjustment: 30 Effective length of query: 287 Effective length of database: 397 Effective search space: 113939 Effective search space used: 113939 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