Align Putrescine transport system permease protein PotI (characterized)
to candidate Pf1N1B4_4350 Putrescine transport system permease protein PotI (TC 3.A.1.11.2)
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4350 Length = 294 Score = 340 bits (871), Expect = 3e-98 Identities = 170/264 (64%), Positives = 209/264 (79%) Query: 15 ILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAAC 74 +L+ G +F+Y PML+LVIYSFN+SKLVTVW GWS +WY LL + +M +V SL IA Sbjct: 10 MLIFGLSFIYLPMLILVIYSFNASKLVTVWGGWSVKWYVGLLDNTQLMGSVVRSLEIACY 69 Query: 75 AATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGW 134 A AA LGT+AA VL R RF+G F ++TAPLVMP+VITGLSLLLLFVA+A IGW Sbjct: 70 TAIAAVALGTLAAFVLTRVTRFKGRTLFGGLVTAPLVMPEVITGLSLLLLFVAMAQLIGW 129 Query: 135 PADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIM 194 P +RG++TIW+AH TFC AYVAVV+S+RLRELD SIEEAAMDLGA P KVFF+IT+PMI Sbjct: 130 PQERGLVTIWIAHTTFCAAYVAVVVSARLRELDLSIEEAAMDLGARPFKVFFLITIPMIA 189 Query: 195 PAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVG 254 P++ +G +++F LSLDDLV+ASFVSGPG+TTLPM VFS+VR+GV PEINA+A+LIL AV Sbjct: 190 PSLAAGGMMSFALSLDDLVLASFVSGPGSTTLPMEVFSAVRLGVKPEINAVASLILLAVS 249 Query: 255 IVGFIAWYLMARAEKQRIRDIQRA 278 +V F+ WY +AE R R IQ A Sbjct: 250 LVTFMVWYFSRKAEATRKRAIQEA 273 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: 268 Number of extensions: 7 Number of successful extensions: 3 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: 294 Length adjustment: 26 Effective length of query: 255 Effective length of database: 268 Effective search space: 68340 Effective search space used: 68340 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