Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AZOBR_RS32385 AZOBR_RS32385 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__azobra:AZOBR_RS32385 Length = 434 Score = 196 bits (498), Expect = 1e-54 Identities = 130/405 (32%), Positives = 197/405 (48%), Gaps = 4/405 (0%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60 + + P P+S++AASA P L V DV V+GAG TGLS+A+ L E G +V VLEA Sbjct: 8 LLDAPLPDSHWAASAVAGPETGPLDGAVRVDVAVVGAGVTGLSTAIHLAEQGVRVVVLEA 67 Query: 61 AKVGFGASGRNGGQIVNSYSR-DIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119 + GFG SGRN GQI+ + SR D + + G + L M ++ + + +YQ++ Sbjct: 68 REPGFGGSGRNNGQIIPTLSRLDPANLTAAYGEAKGAALARMVGGSAALVFDLIERYQMR 127 Query: 120 CD-LKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDM 178 CD ++ G + A +M E + W G ++ LLD + + + G M+ + Sbjct: 128 CDGVQKGWIQPAHRPGRMKAAEQRVAQWRALG-AEVALLDAAQTERALGTRFWHGAMVAL 186 Query: 179 SGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGN 237 +GGH++PL+LA A A LG I+ +P V I R G + TP+G V A +++A N Sbjct: 187 TGGHVNPLSLAREMARAALGLGVAIHSDTPVVSIGRAGTGWTLTTPRGSVTADRVVLATN 246 Query: 238 AYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRL 297 AY +L P L +P + TEPL L S+LP D D L ++R T D RL Sbjct: 247 AYTDDLWPGLRRSVVPVLNFQMVTEPLPAALRASVLPSDMACSDTRGDLHFFRWTADNRL 306 Query: 298 IFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDN 357 + G +V A R ++ + FPQ+ + I +W+G+ +T P L Sbjct: 307 VSGCTLVRSADAERRARERTRERIRRVFPQIGNPAIARSWSGHLAMTADFRPHFHELAPG 366 Query: 358 IYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFP 402 + + G +G G+ G+ LA G A P P P Sbjct: 367 VTGAVGYNGRGMALGTAVGRELARHATGTGAPELALPFTPVKPLP 411 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: 463 Number of extensions: 22 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: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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