Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF5501 PS417_28155 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__WCS417:GFF5501 Length = 363 Score = 437 bits (1124), Expect = e-127 Identities = 213/353 (60%), Positives = 269/353 (76%), Gaps = 2/353 (0%) Query: 15 AGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETG-IKVVYDVYDSNEVLEAKLLAG 73 A ++GMA A + K L VYNW DYI P LE F + IK+VYD++D+NE LEAKLL G Sbjct: 11 AAVISGMAHA-EEKTLRVYNWFDYITPKALEDFKAQNPTIKLVYDIFDTNEALEAKLLTG 69 Query: 74 KSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMW 133 +GYDVVVPSN FLAKQI+AGV+Q LD+S+L NWK+L+ LM +E +DPGN+ A+PYM+ Sbjct: 70 NAGYDVVVPSNVFLAKQIEAGVFQPLDRSQLQNWKHLDPKLMKLIEANDPGNKFAVPYMY 129 Query: 134 GTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLG 193 GTI IG+NPDKVKAA G NAPVDSWDL+FK ENI KLKQCGV+ LDSP+EILP AL +LG Sbjct: 130 GTILIGFNPDKVKAALGVNAPVDSWDLIFKEENISKLKQCGVALLDSPSEILPLALQHLG 189 Query: 194 YKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAE 253 P++ NPK+ AE L LKIRPYVTYFHSSKY++D+ANG+ICVA+GYSG QA +RA Sbjct: 190 LDPNSSNPKDYAKAEALLLKIRPYVTYFHSSKYMADIANGDICVAVGYSGSFSQAANRAR 249 Query: 254 EAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPN 313 +AKN VTV +PKEGA +FDM+AIPK A+N + A F+N+L++P+++A I+D V +PN Sbjct: 250 DAKNGVTVDMRLPKEGAPIWFDMLAIPKGAKNPQDAYTFINYLLQPQVIAPISDFVGYPN 309 Query: 314 GNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366 N AT V +IRN+P +YP+E M LYT L +RA TR+W+KIKSG Sbjct: 310 PNKDATEQVDPSIRNNPNLYPTEAAMATLYTLKPLGRDAERARTRAWSKIKSG 362 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: 466 Number of extensions: 21 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 363 Length adjustment: 30 Effective length of query: 337 Effective length of database: 333 Effective search space: 112221 Effective search space used: 112221 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