Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate GFF5297 PS417_27120 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__WCS417:GFF5297 Length = 364 Score = 421 bits (1083), Expect = e-122 Identities = 198/338 (58%), Positives = 258/338 (76%), Gaps = 1/338 (0%) Query: 30 LHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLEAKLLAGKSGYDVVVPSNSFLAK 89 +H+YNWSDYI DTL F K +GIK VYDV+DSNE LE KLLAG++GYDVVVPSN FL K Sbjct: 28 VHIYNWSDYIGTDTLANFEKASGIKPVYDVFDSNETLEGKLLAGRTGYDVVVPSNHFLGK 87 Query: 90 QIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEHAIPYMWGTIGIGYNPDKVKAAF 149 QIKAG +QKLDKS L N+ NL+ L+ LE +DPGN++A+PY+WGT GIGYN DK K Sbjct: 88 QIKAGAFQKLDKSLLTNYANLDPALLKRLEKNDPGNQYAVPYLWGTNGIGYNGDKGKEVL 147 Query: 150 GDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPAALHYLGYKPDTDNPKELKAAEE 209 G + +DSW ++F+PEN++KL CGVSF+DS E+LPA L+Y+G P++ NP + K AEE Sbjct: 148 GVDH-IDSWAVLFEPENMKKLATCGVSFMDSADEMLPAVLNYMGLNPNSTNPDDYKKAEE 206 Query: 210 LFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQAKSRAEEAKNKVTVKYNIPKEG 269 LK+RPYVTYFHSSKYISDLANGNICVA G+SGD++QAK+RA EA V + Y IPKEG Sbjct: 207 KLLKVRPYVTYFHSSKYISDLANGNICVAAGFSGDVFQAKARAAEAGKGVNIAYTIPKEG 266 Query: 270 AGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITDVVQFPNGNAAATPLVSEAIRND 329 +FD++AIPKDA N + A AF+N+L++PE++A+++D V + N N A L+ ++IR D Sbjct: 267 GNLWFDVLAIPKDATNVKEAHAFINYLLQPEVIAQVSDYVGYANPNPGADKLMEQSIRTD 326 Query: 330 PGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 +YP + V+ + + +LP K QR MTRSWTK+K+GK Sbjct: 327 EAVYPPQAVLDRTFVNFELPPKVQRLMTRSWTKVKTGK 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: 458 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 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