Align putrescine transport system permease protein PotH (characterized)
to candidate WP_083763520.1 AMB_RS13200 putrescine ABC transporter permease PotH
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_000009985.1:WP_083763520.1 Length = 316 Score = 339 bits (870), Expect = 5e-98 Identities = 172/289 (59%), Positives = 214/289 (74%), Gaps = 2/289 (0%) Query: 23 LQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLN 82 L+ + GR LV PY WL+L FL+PFLIV KISL+E IPPY L++WA+G TL Sbjct: 24 LEGRGGRFLVGLAPYAWLLLFFLVPFLIVLKISLSEPQMGIPPYMPLIDWAEGAFKGTL- 82 Query: 83 LGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILP 142 + L D LY AYL SL++A IST CLL+GYP A+A+A + S R LL+LV LP Sbjct: 83 -AGYNTLLGDNLYLLAYLGSLKLAGISTLGCLLLGYPAAYAIARAPQSRRQALLMLVALP 141 Query: 143 SWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLP 202 WTSFLIRVYAW+GILKN G+LN L LG+I +PL IL T+ AV IG+VY+Y+PFM+LP Sbjct: 142 FWTSFLIRVYAWIGILKNEGLLNMALQALGLISEPLQILETSTAVVIGMVYSYLPFMILP 201 Query: 203 IYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELL 262 +Y L ++D SL+EAA DLG RP K F V +PL+ G+IAG MLVFIPAVGEFVIP+LL Sbjct: 202 LYATLEKMDLSLLEAAADLGCRPFKAFLAVTLPLSMPGVIAGCMLVFIPAVGEFVIPDLL 261 Query: 263 GGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQK 311 GGPD+++IG+VLW EFF+NRDWP ASAVA+ ML+LL+VPIM F + K Sbjct: 262 GGPDTLVIGKVLWAEFFDNRDWPTASAVAVAMLVLLVVPIMVFQHFEAK 310 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: 375 Number of extensions: 15 Number of successful extensions: 2 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: 316 Length adjustment: 27 Effective length of query: 290 Effective length of database: 289 Effective search space: 83810 Effective search space used: 83810 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