Align Putrescine transport system permease protein PotI (characterized)
to candidate SMc00773 SMc00773 putrescine ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Smeli:SMc00773 Length = 273 Score = 300 bits (768), Expect = 2e-86 Identities = 152/270 (56%), Positives = 202/270 (74%), Gaps = 6/270 (2%) Query: 9 SPWRIVILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLS 68 S + I ++LGF FLY P+++LVI+SFN SKLVTVWAG+ST+WY +L + ++ A ++ Sbjct: 5 SRFNIASVVLGFGFLYLPIVLLVIFSFNESKLVTVWAGFSTKWYTQLWHNQGLLDAAWVT 64 Query: 69 LTIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVAL 128 + +A +AT A +LGT+AA+ LVR+ RFRG F+ M+ APLVMP+VITGLSLLLLFVA+ Sbjct: 65 IRVALLSATCATVLGTLAALALVRYTRFRGRVLFSGMVYAPLVMPEVITGLSLLLLFVAI 124 Query: 129 AHAIGWPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVI 188 DRG TI LAH+TF +VAVV+ SRL D+SIEEAA+DLGATP++ FF I Sbjct: 125 GF------DRGFWTITLAHITFTMCFVAVVVQSRLLSFDQSIEEAALDLGATPVRTFFAI 178 Query: 189 TLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATL 248 TLP+I PA+ SGW+LAFTLSLDDLVI+SF +GPGATTLPM ++S VR+GV PEINA+ T+ Sbjct: 179 TLPVIAPAVFSGWILAFTLSLDDLVISSFTTGPGATTLPMKIYSQVRLGVTPEINAICTI 238 Query: 249 ILGAVGIVGFIAWYLMARAEKQRIRDIQRA 278 ++G V + +A + R E QR +D + A Sbjct: 239 LIGIVALGVIVASIVTKRREVQREKDERAA 268 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: 283 Number of extensions: 13 Number of successful extensions: 2 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: 273 Length adjustment: 25 Effective length of query: 256 Effective length of database: 248 Effective search space: 63488 Effective search space used: 63488 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