Align Putrescine transport system permease protein PotI (characterized)
to candidate WP_011840777.1 RSPH17029_RS05410 ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >NCBI__GCF_000015985.1:WP_011840777.1 Length = 266 Score = 177 bits (450), Expect = 2e-49 Identities = 92/234 (39%), Positives = 139/234 (59%), Gaps = 3/234 (1%) Query: 18 LGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACAAT 77 L F LYAP+ LV YSFN + +++W G+S RWY + + +A SL IAA A+ Sbjct: 19 LAFLALYAPIFTLVAYSFNDANAISIWGGFSFRWYEAAWANREVQAATARSLVIAASASV 78 Query: 78 AAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPAD 137 A T+AA+ R G FRG I PL++P+++T ++LL++F ++ A G+ Sbjct: 79 IATSAATMAALGTTRRGSFRGQTFIYVAINQPLMVPEIVTAVALLIVFASVKVATGYS-- 136 Query: 138 RGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPAI 197 G+ + LAH FC + + I +RL +D S+E AA DL A P + F +TLP++ P I Sbjct: 137 -GLGYLILAHSAFCIPFAYLPIRARLEGMDLSLETAAADLYANPWQTFRHVTLPLMAPGI 195 Query: 198 ISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILG 251 ++G +LAF +SLDD+VI FV G TLP + +R + PE+NA++T +LG Sbjct: 196 VAGAMLAFVISLDDVVITEFVKSAGQDTLPTYMLGQMRRAITPEVNAISTALLG 249 Lambda K H 0.330 0.140 0.430 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: 194 Number of extensions: 4 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: 281 Length of database: 266 Length adjustment: 25 Effective length of query: 256 Effective length of database: 241 Effective search space: 61696 Effective search space used: 61696 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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