Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_046157099.1 VL52_RS11115 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_000971335.1:WP_046157099.1 Length = 429 Score = 401 bits (1030), Expect = e-116 Identities = 207/425 (48%), Positives = 278/425 (65%), Gaps = 1/425 (0%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 A+ P+P SYYAA+A+ P+P L+ + DVCV+G G GLS+AL L E GF V +LE + Sbjct: 5 AHQPHPPSYYAATAHAWDPQPPLRGEASCDVCVVGGGLAGLSAALNLREKGFSVILLEGS 64 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 VGFGASGRNGGQ++ Y+ D+D I VG + A+ L +M+ E II ERV ++ IQCD Sbjct: 65 HVGFGASGRNGGQVIAGYAGDMDGIRAQVGEEAAKALWDMSVEAVEIIDERVRRHGIQCD 124 Query: 122 LKDGGVFAALTAKQMGHLES-QKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 + G V AA+ + M LE Q+ ER+ + ++L D+ +R +A E Y GG+ D Sbjct: 125 WQRGYVSAAVKPRHMRELEDWQREAEERYDYGGMQLWDRAALRGKLASERYQGGLFDPRS 184 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GH+HPLN LG A A + G I+EQ+PA+RIE+G +P V T G VR + +++A N+Y+ Sbjct: 185 GHLHPLNYTLGLARAALAAGVDIHEQTPALRIEQGDAPKVFTEHGVVRCRHLVLACNSYI 244 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 G L P L + MP GT VIATEPLG+E A +L+ + V D N++LDYYRL+ D RL+FG Sbjct: 245 GALAPRLERRIMPAGTYVIATEPLGEERARALIADNMAVCDTNFVLDYYRLSADHRLLFG 304 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 G V Y +P ++ +R ML+ FPQL DV IDYAW G +T++R P GRL N+YY Sbjct: 305 GKVSYSGHEPRDLAGSMRADMLRVFPQLADVGIDYAWGGFCDITVNRAPDFGRLSGNVYY 364 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420 QG SGHGV T LAGKV+AEA+ G + R D FA + H FPGG+LLRTP +G YY Sbjct: 365 LQGFSGHGVNITGLAGKVVAEAIAGTSSRLDLFAKIRHRDFPGGKLLRTPALVLGMAYYR 424 Query: 421 LRDKL 425 +RD L Sbjct: 425 MRDYL 429 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: 627 Number of extensions: 29 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: 427 Length of database: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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