Align Putrescine transport system permease protein PotI (characterized)
to candidate AO356_25720 AO356_25720 polyamine ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25720 Length = 269 Score = 131 bits (330), Expect = 1e-35 Identities = 81/248 (32%), Positives = 134/248 (54%), Gaps = 8/248 (3%) Query: 22 FLYAPMLMLVIYSFNSSK-LVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACAATAAA 80 FL P++ +V+ SF SS+ LV GW+ +WYG+ + M+A SL +A A Sbjct: 26 FLLLPIVFIVLLSFGSSQWLVFPPPGWTLKWYGQFFSNPDWMNAALTSLKVAVLTTVCAV 85 Query: 81 ILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPADRGM 140 LG A LVR GRF G + T P+++P VI +++ LF+ L + M Sbjct: 86 ALGLPTAFALVR-GRFPGREMLYGLFTLPMIVPLVIIAVAVYALFLKLGYT------GTM 138 Query: 141 LTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPAIISG 200 ++HV + + I + L+ D+SIE+AA+ GA+ L+ F +T P I P +++G Sbjct: 139 FAFVVSHVIVALPFTIISIINSLKLFDQSIEDAAVICGASRLQAVFKVTFPAIRPGMVAG 198 Query: 201 WLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVGIVGFIA 260 L AF +S D++V++ ++ P TLP+ +++++R + P I +TL++G +V IA Sbjct: 199 ALFAFLVSWDEVVLSVMMASPTLQTLPVKMWTTLRQDLTPVIAVASTLLIGLSVLVMVIA 258 Query: 261 WYLMARAE 268 L R E Sbjct: 259 AALRRRNE 266 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: 215 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 281 Length of database: 269 Length adjustment: 25 Effective length of query: 256 Effective length of database: 244 Effective search space: 62464 Effective search space used: 62464 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