Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AO353_09170 AO353_09170 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo3_N2E3:AO353_09170 Length = 437 Score = 386 bits (991), Expect = e-112 Identities = 201/426 (47%), Positives = 269/426 (63%), Gaps = 4/426 (0%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 +N + SYYAAS+ P P PAL+ ++ DVCV+G G++GL++A+ L E G V +LEA Sbjct: 10 SNNRHTASYYAASSLPQPDYPALKGELLADVCVVGGGFSGLNTAIELAERGLNVVLLEAR 69 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 K+G+GASGRNGGQ++ +D +G + + M E ++R+RV +QI CD Sbjct: 70 KIGWGASGRNGGQLIRGVGHGLDQFAEVIGTDGVRQMKLMGLEAVELVRQRVEHFQIVCD 129 Query: 122 LKDGGVFAALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 L G A + + G E L + LL + VV + YVGG++DM Sbjct: 130 LTWGYCDLANKPRDLEGFAEDAAELHSLGYRHETRLLQAHEMHSVVGSDRYVGGLIDMGS 189 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GH+HPLNLALGEAAA + LG ++EQS RI+ G VHT QG VRAK +++ NAYL Sbjct: 190 GHLHPLNLALGEAAAAQQLGVKLFEQSAVTRIDYGNEVKVHTTQGTVRAKTLVLGCNAYL 249 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 NL PEL+ K +P G+ +IATEPL AH+LLPQ+ V D LDYYRL+ D+RL+FG Sbjct: 250 NNLNPELSGKVLPAGSYIIATEPLSAAQAHALLPQNMAVCDQRVALDYYRLSADRRLLFG 309 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NI 358 G Y RDP++I A +RPKML FPQL VKIDY W G + +RLPQ+GRL D N+ Sbjct: 310 GACHYSGRDPSDIAAYMRPKMLDVFPQLAGVKIDYQWGGMIGIGANRLPQIGRLKDQPNV 369 Query: 359 YYSQGCSGHGVTYTHLAGKVLAEALRG-QAERFDAFADLPHYPFPGGQLLRTPFAAMGAW 417 YY+Q SGHG+ THLAGK+LAEA+ G Q FD FA +PH FPGG+ LR+P A+G Sbjct: 370 YYAQAYSGHGLNATHLAGKLLAEAISGQQGGGFDLFAKVPHTTFPGGKYLRSPLLALGML 429 Query: 418 YYGLRD 423 +Y +++ Sbjct: 430 WYRMKE 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: 610 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 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