Align spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD (characterized)
to candidate 209024 DVU0095 polyamine ABC transporter, periplasmic polyamine-binding protein
Query= CharProtDB::CH_088339 (348 letters) >MicrobesOnline__882:209024 Length = 345 Score = 346 bits (887), Expect = e-100 Identities = 166/340 (48%), Positives = 231/340 (67%) Query: 6 RHLLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETM 65 R L L L A + + L +NW+EYVP +L++FTKETGIKV+Y+TYESNE M Sbjct: 3 RLLATVVMLLLWTGVAVSAEPKVLNVFNWSEYVPQTVLDRFTKETGIKVVYTTYESNEAM 62 Query: 66 YAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDY 125 YAK+K + YD+VVPSTY++D MRK+G++ KID++KLTN++NLDP +L++PFDP N++ Sbjct: 63 YAKIKLLRGKGYDIVVPSTYFIDMMRKDGLLAKIDRAKLTNYANLDPRVLHQPFDPQNEF 122 Query: 126 SIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGN 185 S+PY+WG T + VN VDP +++SW DL++PE+KG ++L+DD R+ F +AL+ LGYS N Sbjct: 123 SVPYMWGNTGLMVNRKVVDPATISSWNDLFRPEFKGGVILSDDLRDTFGIALKALGYSVN 182 Query: 186 TTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDV 245 +T EI+AAY L KL P+V F+ ++ EV GM WNG AF+A + Sbjct: 183 STSEAEIKAAYEWLLKLKPSVRVFDVTATKQAFIAEEVKGGMSWNGDAFIAMNENPDLAF 242 Query: 246 VWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLS 305 V+PKEG W+DSLAIP A++K+ A K I+FLLRPD+AK E Y TPNLAA+K+L Sbjct: 243 VYPKEGLPLWVDSLAIPIGAEHKDNAHKFIDFLLRPDIAKLCVEEYNYSTPNLAAQKILD 302 Query: 306 PEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLK 345 A + P +KN E+ N VG A +YE+Y++ LK Sbjct: 303 ARHAQSRATSPTDADLKNSEFTNGVGKALDVYEKYWEMLK 342 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: 444 Number of extensions: 13 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: 345 Length adjustment: 29 Effective length of query: 319 Effective length of database: 316 Effective search space: 100804 Effective search space used: 100804 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