Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_013518247.1 ALIDE2_RS17665 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_000204645.1:WP_013518247.1 Length = 432 Score = 201 bits (511), Expect = 4e-56 Identities = 142/430 (33%), Positives = 213/430 (49%), Gaps = 8/430 (1%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60 +A+ P S +AA+A P PAL V TDV V+GAGYTGLS+AL L E+G +V VL+A Sbjct: 6 IASHPAAPSLWAATAPAAPDTPALGASVSTDVLVVGAGYTGLSTALHLAESGARVCVLDA 65 Query: 61 AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120 G+GASGRNGGQ+ + D D + R G ++A+ L + ++ +A++ I C Sbjct: 66 HAPGWGASGRNGGQVNPTLKYDPDDLVRIYGAERAEPLIDTVSRSADLVYGLIARHAIDC 125 Query: 121 -DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMS 179 ++ G + T + + ++ R WER G ++E+LD+ + + + GG LD Sbjct: 126 APVRAGWLQVGYTQHAVDGMHARARQWERRG-VRVEMLDRAAVAARIGTPAFAGGWLDGR 184 Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQG-KVRAKFIIVAGN 237 G + PL A G A A + LG ++ SP V +ER G + T QG +V+A+ +++ N Sbjct: 185 AGGVQPLAYARGLARAAQGLGVQVHGGSPVVALERQGMHWIATTAQGHRVQAQQVVLGTN 244 Query: 238 AYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRL 297 Y L P LA + + ++AT PLG +LP LL Y+R RL Sbjct: 245 GYTDGLWPGLARTVLAANSFIVATRPLG-PAGDGILPGGETGSTSQRLLLYFRKDAQGRL 303 Query: 298 IFGG-GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD 356 + GG G + P + + R L FPQL ++ +Y W G +T +P + R Sbjct: 304 LMGGRGHFADPQGPQDFSHLERAVAL-MFPQLGPLQYEYRWAGRIAVTRDFMPHLHRPAP 362 Query: 357 NIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGA 416 I + G +G G+ G+ A + G + F P P P L R AA A Sbjct: 363 GITMALGYNGRGIAMATSLGRHAAALVAGSSAAACPFPVTPVQPIPLHGLQRFYIAAGVA 422 Query: 417 WYYGLRDKLG 426 W Y L D+LG Sbjct: 423 W-YSLLDRLG 431 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: 538 Number of extensions: 30 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: 432 Length adjustment: 32 Effective length of query: 395 Effective length of database: 400 Effective search space: 158000 Effective search space used: 158000 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 Apr 09 2024. 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