Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF5415 PS417_27720 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__WCS417:GFF5415 Length = 430 Score = 385 bits (990), Expect = e-111 Identities = 199/428 (46%), Positives = 275/428 (64%), Gaps = 4/428 (0%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 A+ + SYYAAS+ P P L D+ DVCV+G G++GL++AL L E GF V +LEA Sbjct: 3 ASARHTPSYYAASSVAQPDYPVLTGDMTADVCVVGGGFSGLNTALELAERGFSVVLLEAR 62 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 K+ +GASGRNGGQ++ +D +G + + + M E I+RERV ++QI CD Sbjct: 63 KIAWGASGRNGGQLIRGVGHGLDQFANVIGTEGVRQMKLMGLEAVEIVRERVERFQIPCD 122 Query: 122 LKDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMSG 180 L G A ++ + L G+ ++ LL ++ V+ + YVGGM+DM Sbjct: 123 LTWGYCDLANKSRDLQGLAEDAEELRGLGYRHEVRLLHADQMSSVIGSDRYVGGMIDMGS 182 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GH+HPLNLALGEAAA + LG ++EQS RI+ G VHT QG VRAK +++A NAYL Sbjct: 183 GHLHPLNLALGEAAAAQQLGVKLFEQSEVTRIDYGPEVNVHTAQGNVRAKTLVLACNAYL 242 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 +L P L+ K +P G+ +IATEPL + A LLPQ+ V D +DY+RL+ D+RL+FG Sbjct: 243 NDLNPRLSGKVLPAGSYIIATEPLSEAQAVDLLPQNMAVCDQRVTVDYFRLSADRRLLFG 302 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NI 358 G Y RDP +I A +RPKML+ FPQL DVKIDY W G + +RLPQ+GRL D N+ Sbjct: 303 GACHYSGRDPKDIGAYMRPKMLQVFPQLADVKIDYQWGGMIGIGANRLPQIGRLTDQPNV 362 Query: 359 YYSQGCSGHGVTYTHLAGKVLAEALRGQAE-RFDAFADLPHYPFPGGQLLRTPFAAMGAW 417 YY+Q +GHG+ THLAGK+LAEA+ GQ + RFD FA +PH FPGG+ LR+P A+G Sbjct: 363 YYAQAYAGHGLNATHLAGKLLAEAISGQQQGRFDLFAQVPHITFPGGKHLRSPLLALGML 422 Query: 418 YYGLRDKL 425 ++ L++++ Sbjct: 423 WHRLKERM 430 Lambda K H 0.320 0.139 0.421 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: 599 Number of extensions: 28 Number of successful extensions: 4 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: 427 Length of database: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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