Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_090447371.1 BLS63_RS19080 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_900100495.1:WP_090447371.1 Length = 437 Score = 374 bits (959), Expect = e-108 Identities = 199/430 (46%), Positives = 276/430 (64%), Gaps = 10/430 (2%) Query: 3 NTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAK 62 +T + SYYAAS N P L+ + DVC++G G++GLS+A+ L + GF V +LEA + Sbjct: 11 STQHAASYYAASTNRHLAYPPLRGERRVDVCIVGGGFSGLSTAIELAQKGFSVVLLEAHQ 70 Query: 63 VGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDL 122 +G+GASGRNGGQ++ ++ +G + + L M E I+R+RV ++ I CDL Sbjct: 71 IGWGASGRNGGQLIRGVGHGLEQFLPVLGAEGVRALKLMGLEAVEIVRQRVERFAIDCDL 130 Query: 123 KDGGVFAALTAKQMGHL----ESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDM 178 G + L A + GHL E + L + +L LL ++ EVV E YVGG++DM Sbjct: 131 SWG--YCDL-ANKPGHLAGFAEDLEELRDLGYRHELRLLQPGQMHEVVGSERYVGGLIDM 187 Query: 179 SGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNA 238 GH+HPLNLALGEA A +SLG ++E S A RI+ G+ VHT QG VRA +++ NA Sbjct: 188 GSGHLHPLNLALGEAVAAQSLGVQLFEDSAATRIDYGSEVRVHTAQGLVRAAHLVLGCNA 247 Query: 239 YLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLI 298 YLG+L P L + +P G+ +IATEPL + A +L+PQ+ + D LDYYRL+ D+RL+ Sbjct: 248 YLGDLNPALGGQVLPAGSYIIATEPLSEAQAKALIPQNMALCDQRVALDYYRLSADRRLL 307 Query: 299 FGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD-- 356 FGG Y RDPA+I +RPKML FPQL DVKIDY W G + +RLPQ+GRL D Sbjct: 308 FGGACHYSGRDPADIAGYMRPKMLAVFPQLADVKIDYQWGGMIGIGANRLPQIGRLEDQP 367 Query: 357 NIYYSQGCSGHGVTYTHLAGKVLAEALRGQA-ERFDAFADLPHYPFPGGQLLRTPFAAMG 415 N++Y+Q SGHG+ THLAGK+LAEA+ GQA F+ FA +PH FPGG+ LR+P A+G Sbjct: 368 NVFYAQAYSGHGLNATHLAGKLLAEAIAGQAGGGFELFARVPHLTFPGGKYLRSPLLALG 427 Query: 416 AWYYGLRDKL 425 ++ L++ L Sbjct: 428 MLWHRLKELL 437 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: 639 Number of extensions: 31 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: 437 Length adjustment: 32 Effective length of query: 395 Effective length of database: 405 Effective search space: 159975 Effective search space used: 159975 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 24 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