Align putrescine transport system permease protein PotH (characterized)
to candidate 7025947 Shewana3_3095 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__ANA3:7025947 Length = 301 Score = 390 bits (1001), Expect = e-113 Identities = 184/293 (62%), Positives = 235/293 (80%) Query: 21 SQLQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSIT 80 S+L+ GR I+ PY WL+L F LPF IV KIS + A +IPPY ++AD L+I Sbjct: 5 SKLKWLKGRFWTISFPYAWLLLFFALPFAIVLKISFSTAAISIPPYEATFQYADDVLNIF 64 Query: 81 LNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVI 140 L+LGN+L L DD LY+ AYL SL++A IST CL+IGYP+A+A+A + + +LLLLV+ Sbjct: 65 LHLGNYLMLLDDSLYYTAYLSSLKMALISTIGCLIIGYPMAYAIARAPARLQTVLLLLVM 124 Query: 141 LPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMV 200 LPSWTSFLIRVYAWMGIL N G++NN L+WLG+I PL IL+TN+AVYIGI+YAY+PFM+ Sbjct: 125 LPSWTSFLIRVYAWMGILSNTGIINNTLMWLGIISDPLQILNTNIAVYIGIIYAYLPFMI 184 Query: 201 LPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPE 260 LP+Y L+++D SL+EAA DLG+ L TF+ + PL+K G+IAGSMLVFIPAVGEFVIPE Sbjct: 185 LPLYATLVKLDMSLIEAASDLGSSRLNTFWKITFPLSKSGVIAGSMLVFIPAVGEFVIPE 244 Query: 261 LLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSV 313 LLGGPDS+MIG+VLWQEFFNNRDWPVAS++AI+ML LLI+PI FH++Q +S+ Sbjct: 245 LLGGPDSLMIGKVLWQEFFNNRDWPVASSLAIVMLALLIIPITLFHRYQARSL 297 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: 360 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: 301 Length adjustment: 27 Effective length of query: 290 Effective length of database: 274 Effective search space: 79460 Effective search space used: 79460 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