Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 6938544 Sama_2647 oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__SB2B:6938544 Length = 435 Score = 357 bits (916), Expect = e-103 Identities = 178/422 (42%), Positives = 263/422 (62%), Gaps = 4/422 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP+S+Y A+A + P L +E DVCV+G G++GL++A+ L + GF V +LEA +VG+ Sbjct: 12 YPDSFYFATAKELFQYPVLDSAIEVDVCVVGGGFSGLNTAIELRQKGFNVALLEAKRVGW 71 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGG+++ ++ ++G + + M FE I+R+R+A + I CDL G Sbjct: 72 GASGRNGGELIRGIGHGLEQFHNTIGQEGIDAITQMGFEAVEIVRKRIADHNIDCDLAMG 131 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQ-LELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 A+ + M L + + G+ Q ++LL + + +V+ + Y G ++DM GH+H Sbjct: 132 YCDLAVKPRHMAELAEEFEHLKTAGYRQDIKLLQKADLCDVIGSDCYQGALVDMGSGHLH 191 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGN-L 243 PLNLALGEA LG I+E S A I +G P V T +G+V +++++AGNAY+G+ L Sbjct: 192 PLNLALGEARVARELGVQIFEYSAATNIIKGDKPRVITEKGEVNCRYLVLAGNAYIGHKL 251 Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303 P + K +P G+ ++ATEPL EL ++PQ+ D LDY+ L+ D RL+FGG Sbjct: 252 EPYVGGKVLPAGSYLLATEPLSPELQREIIPQNMAFADMRIALDYFHLSADGRLLFGGLC 311 Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYS 361 Y +DP++IEA +RP + + FP+LK V+IDY W G + +RLPQ+GRL D NI+++ Sbjct: 312 TYSGKDPSDIEAALRPNLERVFPKLKGVRIDYQWGGMIGIGANRLPQLGRLPDAPNIFFA 371 Query: 362 QGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGL 421 Q SGHGV TH+ K+LAEA+ GQAERFD FA + H FPGG LR+P A G Y+ Sbjct: 372 QAYSGHGVNATHMMAKLLAEAIAGQAERFDVFAKVKHMTFPGGPALRSPLLAAGMLYHRF 431 Query: 422 RD 423 D Sbjct: 432 MD 433 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: 565 Number of extensions: 29 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: 435 Length adjustment: 32 Effective length of query: 395 Effective length of database: 403 Effective search space: 159185 Effective search space used: 159185 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