Align Putrescine transport system permease protein PotI (characterized)
to candidate 5208464 Shew_0976 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__PV4:5208464 Length = 275 Score = 355 bits (912), Expect = e-103 Identities = 177/252 (70%), Positives = 208/252 (82%) Query: 19 GFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACAATA 78 G FLYAPM +LV YSFN SKLVTVW G+S +WYGEL RDD ++ AV SL +A A+T Sbjct: 18 GMFFLYAPMFILVFYSFNESKLVTVWGGFSAKWYGELFRDDQILDAVATSLKVAFFASTM 77 Query: 79 AAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPADR 138 A ILGT+AA V+ RF R G + MITAPLVMP+VITGLSLLLLFV +A +GWPA+R Sbjct: 78 AVILGTMAAFVMTRFARSWGKMTLSNMITAPLVMPEVITGLSLLLLFVHMADLLGWPAER 137 Query: 139 GMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPAII 198 GMLT+W+AH TFC AYVAVV+SSRLRELD SIEEAA DLGATPLK FF IT+PMI PA+I Sbjct: 138 GMLTVWIAHSTFCAAYVAVVVSSRLRELDMSIEEAAQDLGATPLKTFFHITVPMISPALI 197 Query: 199 SGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVGIVGF 258 +GWLL+F+LSLDDLVIASF SGPGATTLPM+VFSSVRMGV+P+INALATLI+ V ++ F Sbjct: 198 AGWLLSFSLSLDDLVIASFASGPGATTLPMVVFSSVRMGVSPKINALATLIILIVSLIAF 257 Query: 259 IAWYLMARAEKQ 270 I+WYL RA+K+ Sbjct: 258 ISWYLARRADKR 269 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: 289 Number of extensions: 7 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: 275 Length adjustment: 25 Effective length of query: 256 Effective length of database: 250 Effective search space: 64000 Effective search space used: 64000 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 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