Align Putrescine transport system permease protein PotI (characterized)
to candidate PfGW456L13_1567 Spermidine Putrescine ABC transporter permease component potC (TC_3.A.1.11.1)
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1567 Length = 268 Score = 191 bits (484), Expect = 2e-53 Identities = 101/249 (40%), Positives = 157/249 (63%), Gaps = 7/249 (2%) Query: 18 LGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACAAT 77 L + +LYAP+++LV++SFN+++ TVW G+S WY + A+ A G SL IA CA+ Sbjct: 24 LFYLYLYAPIVVLVVFSFNANQSATVWTGFSFDWYRAAFANQALRQAAGNSLLIAVCASM 83 Query: 78 AAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPAD 137 A + T+AA+ R +F+G I PLV+P+++ G++ L LF + ++G+ Sbjct: 84 VATAIATLAALGTSRGAKFKGLQLSMGAIMLPLVLPEIVVGVATLALFSTIGLSLGY--- 140 Query: 138 RGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPAI 197 G L I AH FC + + I +RL ++D S+E+A+ DL A P + F +TLP++MP I Sbjct: 141 -GNLII--AHTVFCIPFAFLPIRARLNDMDLSLEQASADLYAGPWRTFRKVTLPLLMPGI 197 Query: 198 ISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVGIVG 257 SG +LAF +SLD+ VI+ VS G TTLP+ +F +RMGV P++NA++TLILG V ++ Sbjct: 198 FSGLMLAFIVSLDNFVISMMVSQAGTTTLPIFIFGLLRMGVTPDVNAVSTLILG-VSVLF 256 Query: 258 FIAWYLMAR 266 YL+ + Sbjct: 257 VTLSYLLGK 265 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: 213 Number of extensions: 12 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: 268 Length adjustment: 25 Effective length of query: 256 Effective length of database: 243 Effective search space: 62208 Effective search space used: 62208 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