Align Putrescine transport system permease protein PotI (characterized)
to candidate WP_086509875.1 BZY95_RS10485 putrescine ABC transporter permease PotI
Query= SwissProt::P0AFL1 (281 letters) >NCBI__GCF_002151265.1:WP_086509875.1 Length = 280 Score = 367 bits (943), Expect = e-106 Identities = 182/258 (70%), Positives = 220/258 (85%) Query: 14 VILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAA 73 V+L++G FLY PM++LVIYSFN+S+LVTVWAG+STRWY EL RD ++SAV SL IA Sbjct: 11 VMLIVGLLFLYLPMVVLVIYSFNASRLVTVWAGFSTRWYLELFRDQQILSAVWTSLRIAF 70 Query: 74 CAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIG 133 +A+ A LGT+AA V+VRF RFRG + M+TAPLVMP+VITGLSLLLLFV +A IG Sbjct: 71 FSASMAVCLGTLAAFVMVRFTRFRGKTALSSMVTAPLVMPEVITGLSLLLLFVHMAQTIG 130 Query: 134 WPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMI 193 WPADRGM+TIW+AH TFC+AYVAVV++SRLRELD SIEEAAMDLG+ P++ FF ITLPMI Sbjct: 131 WPADRGMVTIWIAHTTFCSAYVAVVVASRLRELDLSIEEAAMDLGSRPVRTFFQITLPMI 190 Query: 194 MPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAV 253 PA+ +GWLLAFTLSLDDLVIASFVSGPGATTLPM+VFSSVR+GV+P+INALATLI+ AV Sbjct: 191 APAVAAGWLLAFTLSLDDLVIASFVSGPGATTLPMVVFSSVRLGVSPKINALATLIILAV 250 Query: 254 GIVGFIAWYLMARAEKQR 271 + F+AWY+M R+E +R Sbjct: 251 SLATFLAWYMMRRSEAKR 268 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: 288 Number of extensions: 8 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: 280 Length adjustment: 26 Effective length of query: 255 Effective length of database: 254 Effective search space: 64770 Effective search space used: 64770 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 Sep 24 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