Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF2636 PS417_13430 spermidine/putrescine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__WCS417:GFF2636 Length = 359 Score = 442 bits (1138), Expect = e-129 Identities = 210/350 (60%), Positives = 263/350 (75%), Gaps = 2/350 (0%) Query: 18 VAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSGY 77 VA + QAA+ + +YNWSDYIAPDT + F KETGI YDVYDSNE L+ KL+ GKSGY Sbjct: 12 VASIGQAAET--VKIYNWSDYIAPDTTKNFQKETGIGFTYDVYDSNETLDGKLMTGKSGY 69 Query: 78 DVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTIG 137 DVV PSN F+A+QI+ G +KLDKS+LPNWKNLN L+ LE +DPGN H PY+WG+ G Sbjct: 70 DVVFPSNHFMARQIQGGALKKLDKSQLPNWKNLNPVLLKALENNDPGNAHGFPYLWGSTG 129 Query: 138 IGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPD 197 IGYN DKVKA GDNAPVDSWDL+FKPEN+ KL++CGV+ LD+ E+LPAAL+YLG Sbjct: 130 IGYNIDKVKAVLGDNAPVDSWDLIFKPENMAKLQKCGVAILDNGPELLPAALNYLGLPHH 189 Query: 198 TDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKN 257 + P++ K AE+L +K+RPYV YFHSSKY +DLANG+ICVA+G+SGDI QA+SRA+EAKN Sbjct: 190 SKKPEDYKKAEDLLMKVRPYVAYFHSSKYTADLANGDICVAVGFSGDILQAESRAKEAKN 249 Query: 258 KVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAA 317 V + YNIPKEGA +FDMVA+P DA N AF+N+L++P++MA IT+ V + NGN A Sbjct: 250 GVNIGYNIPKEGAAIWFDMVAMPADAPNEAAGYAFMNYLLRPQVMASITNYVHYANGNQA 309 Query: 318 ATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 A LV AI+ D IYPS E+M KL+ +P R TR W I++GK Sbjct: 310 ADSLVDPAIKADTKIYPSPEMMGKLFALEAMPLNIDRVRTRVWNTIRTGK 359 Lambda K H 0.315 0.133 0.390 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: 482 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: 367 Length of database: 359 Length adjustment: 29 Effective length of query: 338 Effective length of database: 330 Effective search space: 111540 Effective search space used: 111540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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