Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate WP_090446581.1 BLS63_RS16345 polyamine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >NCBI__GCF_900100495.1:WP_090446581.1 Length = 364 Score = 421 bits (1081), Expect = e-122 Identities = 202/362 (55%), Positives = 264/362 (72%), Gaps = 5/362 (1%) Query: 7 KTLLALTLAGSVAGMA-QAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEV 65 KTLLA A S+ G+A QAA + +++YNW+DYIA DTL +F + TGIK VYDV+DSNE Sbjct: 7 KTLLA---AASLCGLAGQAAAQQAVNIYNWTDYIAEDTLAEFQQATGIKPVYDVFDSNET 63 Query: 66 LEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGN 125 LE KLLAG SGYDVVVPSN FL +QIKAGV+QKLDKS+LP+W NL+ L+ L+ +DPGN Sbjct: 64 LEGKLLAGNSGYDVVVPSNHFLGRQIKAGVFQKLDKSRLPHWNNLDPQLLERLQANDPGN 123 Query: 126 EHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEIL 185 ++A+PY+WGT GIGYN KVKAA G VDSW ++F+PEN+ KL+ CGV+FLDS E Sbjct: 124 QYAVPYLWGTNGIGYNVAKVKAALGIER-VDSWSVLFEPENLAKLQACGVAFLDSADETF 182 Query: 186 PAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDI 245 PA L+YLG P++ K+ K E +RPY+TYFHSS+YISDLANGNIC+A GYSGD+ Sbjct: 183 PAMLNYLGLDPNSSRTKDYKLVERKLQALRPYITYFHSSRYISDLANGNICIAFGYSGDV 242 Query: 246 YQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEI 305 +QA SRAEEA + + + Y +P+EG +FDM+ IP DA N E A AF+++L++PE++A I Sbjct: 243 FQAMSRAEEAGSGIEIAYVVPREGGNLWFDMLTIPADARNVEQAHAFIDYLLRPEVVARI 302 Query: 306 TDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKS 365 ++ V + N N A L+ +R DP IYP V +LY +LP R MTR+W K+KS Sbjct: 303 SEYVGYANANTRADALMEAQVRQDPSIYPPASVQARLYVSSELPPDAMRWMTRAWNKLKS 362 Query: 366 GK 367 G+ Sbjct: 363 GR 364 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: 470 Number of extensions: 15 Number of successful extensions: 2 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: 364 Length adjustment: 30 Effective length of query: 337 Effective length of database: 334 Effective search space: 112558 Effective search space used: 112558 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 24 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