Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate HSERO_RS05840 HSERO_RS05840 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__HerbieS:HSERO_RS05840 Length = 433 Score = 197 bits (502), Expect = 4e-55 Identities = 138/424 (32%), Positives = 201/424 (47%), Gaps = 9/424 (2%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 +N +P S +AA+A P LQ DV ++GAGYTGLS+AL L + G V VL+A Sbjct: 5 SNPAFPPSLWAATAGEFSGAPPLQASARYDVAIVGAGYTGLSTALHLAQAGVSVCVLDAH 64 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 G+GASGRNGGQ++ D D + G A L + + +A++ I+C+ Sbjct: 65 APGWGASGRNGGQVIPGLKYDPDQLRVMFGSAVADPLIAAIGSAADTVFDLIARHGIECE 124 Query: 122 LKDGG-VFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 + G + + K M LE++ R W G +L+D + + YVGG D Sbjct: 125 AQRAGWIQPTHSPKMMRALEARARQWMAEG-APAQLMDGAEVTRRIGTGAYVGGWKDERA 183 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASP-VVHTPQGK----VRAKFIIVA 235 G +HPL G A A + LG VI+ + R+ER +H P G+ + A+ +++A Sbjct: 184 GSLHPLKYCRGLAQAAQRLGVVIHGDTRVTRLERRQGGWRLHGPSGEQGPHIDAERVVLA 243 Query: 236 GNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDK 295 N Y +L P L + + ++AT PL L S+LP D LL YYR Sbjct: 244 TNGYTDDLWPHLRQSVIAANSFIVATRPLPPALGASILPGGEVTSDSRRLLLYYRRDAQG 303 Query: 296 RLIFGGGVVYG-ARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRL 354 RL+ GG +G + PA+ + R L FPQL V+ +Y W+G +T LP V Sbjct: 304 RLLMGGRGPFGEPQGPADFAHLERSVAL-LFPQLAGVEYEYRWSGRVAITRDFLPHVHEP 362 Query: 355 GDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAM 414 + + G +G G+ + G+ LA+ L G A F P P L R AA Sbjct: 363 APGLSIALGYNGRGIAMATMMGQRLAQRLIGPAGTAFPFPVSTIAPIPLHGLQRFYIAAG 422 Query: 415 GAWY 418 AWY Sbjct: 423 VAWY 426 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: 512 Number of extensions: 26 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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