Align Putrescine transport system permease protein PotI (characterized)
to candidate 7025946 Shewana3_3094 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__ANA3:7025946 Length = 271 Score = 349 bits (896), Expect = e-101 Identities = 173/257 (67%), Positives = 211/257 (82%) Query: 14 VILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAA 73 V+L G FLYAPML+LVIYSFN SKLVTVW G+S +WYGEL D ++ AV SL IA Sbjct: 9 VMLWFGLFFLYAPMLILVIYSFNESKLVTVWGGFSPKWYGELFADQQILDAVWTSLRIAF 68 Query: 74 CAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIG 133 ++T A I+GT+AA V+ RF R + MITAPLVMP+VITGLSLLLLFV +A +G Sbjct: 69 YSSTMAVIIGTMAAFVMTRFKRSWAKLTLSNMITAPLVMPEVITGLSLLLLFVHMADLLG 128 Query: 134 WPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMI 193 WP +RGM+T+W+AH TFC AYVAVV+SSRLRELD SIEEAAMDLGATPLK FF+IT+PMI Sbjct: 129 WPKERGMVTVWIAHSTFCAAYVAVVVSSRLRELDMSIEEAAMDLGATPLKTFFLITVPMI 188 Query: 194 MPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAV 253 PA+++GWLL+F+LSLDDLVIASF SGPGATTLPM+VFSSVR+GV+P+INALATLI+ V Sbjct: 189 SPALVAGWLLSFSLSLDDLVIASFASGPGATTLPMVVFSSVRLGVSPKINALATLIILCV 248 Query: 254 GIVGFIAWYLMARAEKQ 270 ++ F++WY+ RAEK+ Sbjct: 249 SLIAFLSWYMARRAEKR 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: 303 Number of extensions: 10 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: 271 Length adjustment: 25 Effective length of query: 256 Effective length of database: 246 Effective search space: 62976 Effective search space used: 62976 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