Align Putrescine transport system permease protein PotI (characterized)
to candidate PP_1482 PP_1482 polyamine ABC transporter, permease protein
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Putida:PP_1482 Length = 268 Score = 124 bits (311), Expect = 2e-33 Identities = 77/247 (31%), Positives = 129/247 (52%), Gaps = 9/247 (3%) Query: 19 GFTFLYAPMLMLVIYSFNSSKLVTVWA--GWSTRWYGELLRDDAMMSAVGLSLTIAACAA 76 G FL+ P+L++ +Y+FN+ + G++ +W ++ A+ LSL +A A Sbjct: 17 GLLFLHFPILIIFLYAFNTEDAAFSFPPKGFTLKWIDVAFTRPDVLEAIKLSLQVACLAT 76 Query: 77 TAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWPA 136 A +LGT+A+ L R F G + ++ P+ +P +ITG++LL F L Sbjct: 77 LIALVLGTLASAALYRRSFF-GKESISLVLILPIALPGIITGIALLSAFKTLG------I 129 Query: 137 DRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMPA 196 + G+ TI + H TFC V + +RLR +S+ EA+MDLGA + F I LP + A Sbjct: 130 EPGVFTIVVGHATFCVVIVYNNVIARLRRTSQSLIEASMDLGADGWQTFRYIVLPNLGSA 189 Query: 197 IISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAVGIV 256 +++G +LAF LS D++++ +F +G T L+ R P N +A L++ + Sbjct: 190 LLAGGMLAFALSFDEIIVTTFTAGHERTLPIWLLNQLSRPRDVPVTNVVAMLVMLVTMLP 249 Query: 257 GFIAWYL 263 A+YL Sbjct: 250 ILGAYYL 256 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: 178 Number of extensions: 8 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