Align Putrescine transport system permease protein PotI (characterized)
to candidate AZOBR_RS08830 AZOBR_RS08830 putrescine/spermidine ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__azobra:AZOBR_RS08830 Length = 277 Score = 346 bits (887), Expect = e-100 Identities = 174/266 (65%), Positives = 212/266 (79%) Query: 16 LLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACA 75 L G+ FLY P+ +L+ YSFN S+LVTVW G+ST+WY ELL++D ++ A LSL +AA + Sbjct: 11 LWFGYAFLYVPIALLIFYSFNESRLVTVWGGFSTKWYAELLQNDQLLGAAWLSLKVAAMS 70 Query: 76 ATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWP 135 ATA+ +LGT+A + L RFGRFRG F MITAPLVMP+VITGLSLLLLFVAL AIGWP Sbjct: 71 ATASVVLGTVAGLALARFGRFRGRTLFGGMITAPLVMPEVITGLSLLLLFVALEQAIGWP 130 Query: 136 ADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMP 195 RGM TI +AH TF AYVAV+I SRL LD S+EEAAMDLGA P KVFFVITLP+I P Sbjct: 131 DGRGMTTITIAHTTFTMAYVAVIIQSRLVSLDESLEEAAMDLGARPAKVFFVITLPIIAP 190 Query: 196 AIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVGI 255 AI+SGWLLAFTLSLDD+V+ASFVSGPG+TTLPM++FSSV+ G++P+INALATL++ V Sbjct: 191 AIVSGWLLAFTLSLDDVVVASFVSGPGSTTLPMVIFSSVKFGISPQINALATLMMVVVAT 250 Query: 256 VGFIAWYLMARAEKQRIRDIQRARRG 281 FIA +MAR ++QR RD Q A +G Sbjct: 251 GIFIASLVMARQDRQRKRDEQMAVQG 276 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: 282 Number of extensions: 6 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: 277 Length adjustment: 26 Effective length of query: 255 Effective length of database: 251 Effective search space: 64005 Effective search space used: 64005 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