Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate BPHYT_RS13575 BPHYT_RS13575 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__BFirm:BPHYT_RS13575 Length = 430 Score = 209 bits (533), Expect = 1e-58 Identities = 140/418 (33%), Positives = 213/418 (50%), Gaps = 7/418 (1%) Query: 5 PYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVG 64 P P S +AA+A P P L + DV ++GAGYTGLS+AL L E G +V V++A + G Sbjct: 9 PLPPSLWAATAEPAVVTPPLDNSTVVDVAIVGAGYTGLSTALHLAEQGLRVCVIDANEPG 68 Query: 65 FGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD-LK 123 +GASGRNGGQ++ D D + R GP+ L MA + + VA++ I+CD + Sbjct: 69 WGASGRNGGQVIPGLKYDPDELIRRYGPRDGNALVQMAGGAADTVFDLVARHGIRCDATR 128 Query: 124 DGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHI 183 G + + K + L ++ WE G +ELLD+ ++ + + + +VGG +D G + Sbjct: 129 AGWIQPTHSHKLLKTLYARAGQWEARG-APVELLDRAQVSKRLGTDAFVGGWVDRRAGSV 187 Query: 184 HPLNLALGEAAAVESLGGVIYEQSPAVRIERGASP-VVHTPQGKV-RAKFIIVAGNAYLG 241 PL+ A G A A ++ G I+ + A IERGA+ + T G V +K +++A N Y Sbjct: 188 QPLSYARGLARAAQAAGAQIHGGTRAAGIERGANGWRIRTAHGPVIESKQVLLATNGYTD 247 Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301 L P LA + + ++AT+PL D++ ++L D LL Y+R D RL+ GG Sbjct: 248 GLWPRLAQSVIAANSFIVATKPLADDVGATILAGGEVASDSRRLLLYFRKDADGRLLMGG 307 Query: 302 -GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 G R+ A+ + R L FPQL+ + ++ W G +T + LP V + Sbjct: 308 RGPFREPRNAADWAHLERAAQL-MFPQLRGTEYEFRWAGRIAITRNFLPHVHMPAKGMTI 366 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418 + G +G G+ GK LA L G A+ P P P L R +A AWY Sbjct: 367 ALGYNGRGIAMATTLGKHLAAYLGGAAKGL-PLPPTPIEPVPLHALQRFYISAGVAWY 423 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: 507 Number of extensions: 33 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: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 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