Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate AO356_13160 AO356_13160 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13160 Length = 365 Score = 429 bits (1102), Expect = e-125 Identities = 210/356 (58%), Positives = 270/356 (75%), Gaps = 7/356 (1%) Query: 12 LTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLL 71 LTLA SV QAA +H+YNWSDYI TL F K TGIK VYDV+DSNE LE KLL Sbjct: 17 LTLAVSV----QAAST--VHIYNWSDYIGETTLADFEKATGIKPVYDVFDSNETLEGKLL 70 Query: 72 AGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPY 131 AG++GYDVVVPSN FL KQIKAG +QKLDK++LPN+ NL+ L+ LE +DPGN++A+PY Sbjct: 71 AGRTGYDVVVPSNHFLGKQIKAGAFQKLDKAQLPNYANLDPVLLKRLEKNDPGNQYAVPY 130 Query: 132 MWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHY 191 +WGT GIGYN +K+KA G +DSW ++F+PENI+KL CGVSFLDS E++PA L+Y Sbjct: 131 LWGTNGIGYNVEKIKAVLGVEK-IDSWAMLFEPENIKKLSSCGVSFLDSGDEMIPAMLNY 189 Query: 192 LGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSR 251 LG P++++P++ K AE LKIRPYVTYF+SSKYISDLANG ICVA G+SGDI+QA++R Sbjct: 190 LGLNPNSEDPEDYKKAEAQLLKIRPYVTYFNSSKYISDLANGEICVAAGFSGDIFQARAR 249 Query: 252 AEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQF 311 A EA V + Y IPKEG +FDM+AIP+DA N + A AF+N+++KPE++A+++DVV + Sbjct: 250 ASEAGKGVNIAYVIPKEGGNLWFDMLAIPRDATNVKQAHAFINYVLKPEVIAQVSDVVGY 309 Query: 312 PNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 N N A L+ + +R D +YP + V+ KLY +LP K QR MTRSWTK+KSGK Sbjct: 310 ANPNPKAGELMDQKVRTDEAVYPPQAVVDKLYVNSELPPKIQRLMTRSWTKVKSGK 365 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: 457 Number of extensions: 14 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: 365 Length adjustment: 30 Effective length of query: 337 Effective length of database: 335 Effective search space: 112895 Effective search space used: 112895 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