Align spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD (characterized)
to candidate BWI76_RS11240 BWI76_RS11240 spermidine/putrescine ABC transporter substrate-binding protein PotD
Query= CharProtDB::CH_088339 (348 letters) >FitnessBrowser__Koxy:BWI76_RS11240 Length = 348 Score = 669 bits (1727), Expect = 0.0 Identities = 316/348 (90%), Positives = 340/348 (97%) Query: 1 MKKWSRHLLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYE 60 MKKWSRHLLAAGALA+GMSAAHADD+ TLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYE Sbjct: 1 MKKWSRHLLAAGALAVGMSAAHADDSKTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYE 60 Query: 61 SNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFD 120 SNETMYAKLKTYKDGAYDLVVPSTY+VDKMRKEGM+QKIDKSKL+NF NLDP+MLNKPFD Sbjct: 61 SNETMYAKLKTYKDGAYDLVVPSTYFVDKMRKEGMLQKIDKSKLSNFGNLDPEMLNKPFD 120 Query: 121 PNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKL 180 PNNDYSIPYIWGATAIG+N D +DPK+VTSWADLWKPEYK SLLLTDDAREVFQ+ALRKL Sbjct: 121 PNNDYSIPYIWGATAIGINSDEIDPKTVTSWADLWKPEYKSSLLLTDDAREVFQVALRKL 180 Query: 181 GYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAG 240 GYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGM+WNGSA+VARQAG Sbjct: 181 GYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMVWNGSAWVARQAG 240 Query: 241 TPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAA 300 TP++VVWPKEGGIFWMDSL+IPANAKN +GALKLINFLLRP++AKQVAETIGYPTPNLAA Sbjct: 241 TPLEVVWPKEGGIFWMDSLSIPANAKNVDGALKLINFLLRPEIAKQVAETIGYPTPNLAA 300 Query: 301 RKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR 348 RK+LSPEVANDK+LYPDA TI+ GEWQNDVG+AS++YEEYYQKLKAGR Sbjct: 301 RKMLSPEVANDKSLYPDAATIQKGEWQNDVGSASTLYEEYYQKLKAGR 348 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: 605 Number of extensions: 18 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: 348 Length adjustment: 29 Effective length of query: 319 Effective length of database: 319 Effective search space: 101761 Effective search space used: 101761 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