Align putrescine transport system permease protein PotH (characterized)
to candidate GFF959 HP15_938 spermidine/putrescine ABC transporter, permease protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Marino:GFF959 Length = 293 Score = 388 bits (997), Expect = e-113 Identities = 182/293 (62%), Positives = 234/293 (79%) Query: 25 MKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLG 84 M R++V +P++WL+L FLLPF +V KISL AIPPY + W D LS+ +N+G Sbjct: 1 MLFNRRVVFGIPFLWLLLFFLLPFALVLKISLTSAVMAIPPYEPVFRWVDNTLSVVVNIG 60 Query: 85 NFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSW 144 N+L L D LYF AY S++ A ++T CLLIGYP+A+A+A + + +LLL+V+LPSW Sbjct: 61 NYLFLLSDSLYFAAYWGSVKTAFLATVMCLLIGYPMAYAMARTPKHWQLVLLLMVMLPSW 120 Query: 145 TSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIY 204 TSFLIRVYAWMGIL N G+LN+FL+WLG IDQPL +L+TN AV +GIVYAY+PFMVLPIY Sbjct: 121 TSFLIRVYAWMGILGNQGLLNSFLMWLGFIDQPLKMLNTNFAVVLGIVYAYLPFMVLPIY 180 Query: 205 TALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGG 264 T L+++D L+EAA DLG R L TF+ + +PL+K GI+AGSMLVFIPAVGEFVIPELLGG Sbjct: 181 TNLVKLDVRLLEAASDLGCRSLTTFWAITLPLSKAGILAGSMLVFIPAVGEFVIPELLGG 240 Query: 265 PDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSVGEHG 317 PD++MIG+VLW+EFFNNRDWPVASA+AI+MLLLL+VPI+ FH+ Q + + +HG Sbjct: 241 PDTLMIGKVLWEEFFNNRDWPVASALAIVMLLLLLVPIVLFHRFQAREMEKHG 293 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: 364 Number of extensions: 11 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: 293 Length adjustment: 27 Effective length of query: 290 Effective length of database: 266 Effective search space: 77140 Effective search space used: 77140 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