Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 201209 SO2052 hypothetical oxidoreductase (NCBI ptt file)
Query= reanno::pseudo6_N2E2:Pf6N2E2_80 (394 letters) >FitnessBrowser__MR1:201209 Length = 429 Score = 296 bits (757), Expect = 1e-84 Identities = 156/397 (39%), Positives = 234/397 (58%), Gaps = 10/397 (2%) Query: 1 VIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDV---IERSV 57 +IG G+TG+++A+ L E G+KV +LEA K+ +GA+GRNGGQ+ S S D + + R + Sbjct: 33 IIGGGFTGVATAVELSEKGYKVALLEANKIAWGATGRNGGQVTGSLSGDAAMTKQLRRHL 92 Query: 58 GPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVFAALTAKQMGHLESQKRLWERFG 117 G + N+ + G II+ RVAKY I CDLK G + TA GH++ +++++ Sbjct: 93 GQDAEDYVWNLRWRGHDIIKNRVAKYGIDCDLKFGHI---QTAYHPGHMQELQQMFDEAN 149 Query: 118 HTQL----ELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIYEQ 173 + L+ + + +A Y GG+++ H+H +NL LGEA A SLG I+E Sbjct: 150 RRGMGEFMTLVPAQEMSAYLASPLYHGGLVNRRNMHLHSVNLCLGEARAAASLGAQIFEH 209 Query: 174 SPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATEPLGD 233 S + I++ V TP+G V+A +++AGNAY P+L P AT L + Sbjct: 210 SQVLDIQQAELATVVTPKGTVKANSVLIAGNAYHKLGRPKLRGMLFPASLGNCATAKLPE 269 Query: 234 ELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFP 293 ELA L PQ+ V DC ++LDYYRLT D RL+FGGG Y RDP N+ A +RP + + FP Sbjct: 270 ELAKQLNPQNLAVYDCRFVLDYYRLTADNRLMFGGGTNYSGRDPKNVAAELRPAIERTFP 329 Query: 294 QLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQ 353 QLK V I++AW G + ++R+PQ+G++ NI+Y QG SGHGV +H+ +++ +A+ GQ Sbjct: 330 QLKGVDIEFAWAGMAGIVINRIPQLGKISPNIFYCQGYSGHGVATSHIMAEIMGQAIDGQ 389 Query: 354 AERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 390 + FD FA + H P + A+G YY LR+ Sbjct: 390 MQEFDLFAAMRHIRIPLNEWFGNQALALGMLYYTLRE 426 Lambda K H 0.321 0.140 0.423 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: 533 Number of extensions: 24 Number of successful extensions: 3 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: 394 Length of database: 429 Length adjustment: 31 Effective length of query: 363 Effective length of database: 398 Effective search space: 144474 Effective search space used: 144474 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: 50 (23.9 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