Align Putrescine transport system permease protein PotI (characterized)
to candidate 8502261 DvMF_2971 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Miya:8502261 Length = 286 Score = 122 bits (305), Expect = 1e-32 Identities = 83/268 (30%), Positives = 141/268 (52%), Gaps = 21/268 (7%) Query: 18 LGFTFLYAPMLMLVIYSFNSSKLVTV-WAGWSTRWY-------GELLRDDAMMSAVGLSL 69 L F FL+AP+ + + +FN S+ ++ W G++ W+ + D +S++ S Sbjct: 21 LYFVFLFAPLAVTCVLAFNDSQFPSLPWKGFTLDWFLADLPARTGIFHDRGNLSSIFTSA 80 Query: 70 TIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVA-- 127 A + A ++GT AA + + F F++ APLV+P VI G+S+L+ Sbjct: 81 QTAILVSALATLVGTCAAFLFEQ-EEFPLKGALYFLMLAPLVVPGVILGISILIAATTAG 139 Query: 128 --LAHAIGWPADRGMLT-----IWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGAT 180 + +G D G+L + L +F T +V +V+S+RL++ DR++EEAA++LGAT Sbjct: 140 TFMEDVLG--IDVGILRPGFWLVVLGQFSFITTFVTLVVSARLKKFDRTLEEAALNLGAT 197 Query: 181 PLKVFFVITLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNP 240 L+V ITLP + AII +AF +S ++ F+ G TLP+ ++ VR G P Sbjct: 198 RLEVIRYITLPFLRTAIIGAGAVAFLMSFENFNTTLFLVG-SEPTLPINLYLQVRDGSTP 256 Query: 241 EINALATLILGAVGIVGFIAWYLMARAE 268 INA++ L++ +V + Y + E Sbjct: 257 VINAISFLLIVGTSLVACVNLYAGRKPE 284 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: 208 Number of extensions: 15 Number of successful extensions: 4 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: 286 Length adjustment: 26 Effective length of query: 255 Effective length of database: 260 Effective search space: 66300 Effective search space used: 66300 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