Align spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD (characterized)
to candidate 8501223 DvMF_1957 extracellular solute-binding protein family 1 (RefSeq)
Query= CharProtDB::CH_088339 (348 letters) >FitnessBrowser__Miya:8501223 Length = 358 Score = 357 bits (917), Expect = e-103 Identities = 172/339 (50%), Positives = 232/339 (68%) Query: 9 LAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAK 68 LA A L A A + L+ YNW+EYVP +L++FTKETGIKV+Y+TYESNE MYAK Sbjct: 19 LAVLAATLFAGPAVAAEEKVLHVYNWSEYVPQSVLDRFTKETGIKVVYTTYESNEAMYAK 78 Query: 69 LKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIP 128 +K K YD+VVPSTY++ MR +G++ +IDKSKL NF NL P +LN+PFDP N+YS+P Sbjct: 79 VKLLKGVGYDVVVPSTYFISMMRDDGLLARIDKSKLKNFKNLSPKVLNQPFDPGNEYSVP 138 Query: 129 YIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTD 188 Y+WG+ + VN VDP S+TSW DL +PE+ G ++L+DD R+ +AL+ LGYS N+T+ Sbjct: 139 YMWGSAGLMVNRKVVDPASITSWNDLNRPEFAGKVILSDDQRDSMGVALKALGYSVNSTN 198 Query: 189 PKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWP 248 EI+AAY LKKL+P V F+ ++ EV G+IWNG A++A + V+P Sbjct: 199 EAEIKAAYEWLKKLLPAVRVFDVTASKQAFISEEVAAGLIWNGDAYIAASENENLVYVYP 258 Query: 249 KEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEV 308 +EG W+DSLAIP AK+K+ A K I+FLLRPDVAK+ E Y TPN+ A+K+LSPE+ Sbjct: 259 REGVPLWVDSLAIPVGAKHKDNAHKFIDFLLRPDVAKECVEEYNYSTPNVGAQKILSPEL 318 Query: 309 ANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAG 347 A + P +KN E+ N VG A IYE+Y++ LK G Sbjct: 319 AKSRITSPSDADLKNAEFTNSVGNALEIYEKYWEMLKTG 357 Lambda K H 0.314 0.132 0.397 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: 434 Number of extensions: 12 Number of successful extensions: 1 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: 348 Length of database: 358 Length adjustment: 29 Effective length of query: 319 Effective length of database: 329 Effective search space: 104951 Effective search space used: 104951 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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