Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate WP_086509878.1 BZY95_RS10500 polyamine ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >NCBI__GCF_002151265.1:WP_086509878.1 Length = 367 Score = 409 bits (1050), Expect = e-119 Identities = 205/362 (56%), Positives = 257/362 (70%), Gaps = 3/362 (0%) Query: 7 KTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVL 66 K LA+ L GS+A A A + VYNWSDYIAPDTLEKFT+ TGI+V+YDVYDSNEVL Sbjct: 6 KLSLAVAL-GSLAMAAAAVQANEVRVYNWSDYIAPDTLEKFTEATGIRVIYDVYDSNEVL 64 Query: 67 EAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNE 126 +A +LAG+SGYDVVVPSN +L +QI AGVYQ+LD KLPN NLN +L+ LE DPG+ Sbjct: 65 DAAMLAGRSGYDVVVPSNHYLTRQISAGVYQELDHDKLPNMANLNPELLDDLEFIDPGSR 124 Query: 127 HAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQ--CGVSFLDSPTEI 184 ++IPYMWGT GIGYN ++V G++AP+DSW L+F PE L+Q CG+S LDS E+ Sbjct: 125 YSIPYMWGTNGIGYNVERVTEILGEDAPLDSWALIFDPEITTALRQGGCGISMLDSGDEM 184 Query: 185 LPAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGD 244 L A+ YLG P ++ +L+AA +L +R +TYFHSS+YISDLANG+ICVA GYSGD Sbjct: 185 LSPAMAYLGLSPLSEETADLEAAGDLIAAVRDNITYFHSSRYISDLANGDICVAAGYSGD 244 Query: 245 IYQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAE 304 I+QA RAEEA T+ Y IPKEGA +FDM+AIP DA N + A AF+NF+++PEI A Sbjct: 245 IFQAADRAEEAGRDFTIDYIIPKEGAALWFDMMAIPADAPNPDNAHAFINFILEPEIAAA 304 Query: 305 ITDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIK 364 IT+ V + N N AA + I NDP IYP +EVM LY + P QR TR W ++K Sbjct: 305 ITEYVVYANPNIAANEYLDPDILNDPAIYPDQEVMDNLYVAEEKPLAVQRVRTRVWNRVK 364 Query: 365 SG 366 SG Sbjct: 365 SG 366 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: 459 Number of extensions: 27 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: 367 Length adjustment: 30 Effective length of query: 337 Effective length of database: 337 Effective search space: 113569 Effective search space used: 113569 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