Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate Pf6N2E2_4388 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4388 Length = 437 Score = 382 bits (981), Expect = e-110 Identities = 200/419 (47%), Positives = 264/419 (63%), Gaps = 4/419 (0%) Query: 9 SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68 SYYAAS+ P P P LQ ++ DVCV+G G++GL++A+ L E G V +LEA ++G+GAS Sbjct: 17 SYYAASSLPQPDHPLLQGELLADVCVVGGGFSGLNTAIELAERGMSVVLLEAHRIGWGAS 76 Query: 69 GRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVF 128 GRNGGQ++ +D +G + + M E I+R+RV ++QI CDL G Sbjct: 77 GRNGGQLIRGVGHGLDQFAPIIGADGVRQMKLMGLEAVEIVRQRVERFQIPCDLTWGYCD 136 Query: 129 AALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLN 187 A + G E + L LL + VV + YVGG++DM GH+HPLN Sbjct: 137 LANKPSDLEGFAEDAEELRSLGYRHPTRLLQANEMHSVVGSDRYVGGLIDMGSGHLHPLN 196 Query: 188 LALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPEL 247 LALGEAAA + LG ++EQS RI+ G VHT QG VRAK +++ NAYL L P+L Sbjct: 197 LALGEAAAAQQLGVRLFEQSAVTRIDYGPEVKVHTQQGSVRAKTLVLGCNAYLNGLNPQL 256 Query: 248 AAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGA 307 K +P G+ +IATEPL A +LLPQ+ V D LDYYRL+ D+RL+FGG Y Sbjct: 257 GGKVLPAGSYIIATEPLSQAQAQALLPQNMAVCDQRVALDYYRLSADRRLLFGGACHYSG 316 Query: 308 RDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYSQGCS 365 RDP +I A +RPKMLK FPQL DVKIDY W G + +RLPQ+GRL D N+YY+Q S Sbjct: 317 RDPQDIGAYMRPKMLKVFPQLADVKIDYQWGGMIGIGANRLPQIGRLKDQPNVYYAQAYS 376 Query: 366 GHGVTYTHLAGKVLAEALRGQ-AERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 GHGV THLAGK+LAEA+ GQ + FD FA +PH FPGG+ LR+P A+G ++ L++ Sbjct: 377 GHGVNATHLAGKLLAEAISGQHSSGFDLFAQVPHMTFPGGKHLRSPLLALGMLWHRLKE 435 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: 617 Number of extensions: 35 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 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