Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 6938339 Sama_2458 FAD dependent oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__SB2B:6938339 Length = 442 Score = 155 bits (392), Expect = 2e-42 Identities = 136/430 (31%), Positives = 202/430 (46%), Gaps = 21/430 (4%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFL-LENGFKVTVLEA 60 A P ++++ + P+P P LQ ++TDV VIG G+TGL +A +L E G +VT+LEA Sbjct: 11 AQQALPSTFWSGTTEPLPESPRLQGHLQTDVIVIGGGFTGLLTAYYLATEYGRQVTLLEA 70 Query: 61 AKVGFGASGRNGGQIVNSYSR-DIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119 ++GFGAS RNGG ++ R + + A+ + E + + +I Sbjct: 71 NRIGFGASARNGGFVLKGSGRLGYGQMAKRWDLDTAKGIYQEFSEAVARVEGLIQDGKID 130 Query: 120 CDLKDGGVF-AALTAKQMGHLESQKRLWERFGHTQLELLDQRRIR-EVVACEEYVGGMLD 177 C+ ++ G A + K M L++ R E + R+R + + + G + Sbjct: 131 CNPQEKGYLKIAHSPKAMKTLQAGADFIARHMGQGAEFICPARLRIDYLNHHQSYGALRL 190 Query: 178 MSGGHIHPLNLALGEAAAVESLGGVIYEQS---PAVRIERGASPVVHTPQGKVRAKFIIV 234 G ++PL L G A G I+EQS +VR +G S + T G++ A ++ Sbjct: 191 ADGFGLNPLKLLQGYARLAREAGVQIFEQSTVLASVRTAKGFS--LETEAGRIDANAMVF 248 Query: 235 AGNAYL-GNLVPELAAKSMPCGTQVIATEPLGDE-LAHSLLPQDYCVEDCNYLLDYYRLT 292 AGNAY L L + +P + VI TEPL + LA + L D L YYRL Sbjct: 249 AGNAYTQPGLTETLTGRFLPILSNVIVTEPLSEAVLAEAGLYSRQVAMDTRILKYYYRLL 308 Query: 293 GDKRLIFGG-GVVYGARDPAN--IEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLP 349 + RL+FGG G V+G RD N A ++ M KAFP L DV + + W G +L +P Sbjct: 309 PENRLLFGGRGAVWG-RDADNSVYPARLKEAMNKAFPALTDVGLSHTWHGWLAASLDDMP 367 Query: 350 QVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRT 409 V G YS G G GV+++ A LA L G+A LP Y P Sbjct: 368 HVYTRGGE-GYSLGYCGAGVSFSSQAAWRLAGMLSGKAA-----PSLPLYGTPLPAFPLA 421 Query: 410 PFAAMGAWYY 419 P +G W + Sbjct: 422 PLRRVGQWAF 431 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: 549 Number of extensions: 31 Number of successful extensions: 7 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: 442 Length adjustment: 32 Effective length of query: 395 Effective length of database: 410 Effective search space: 161950 Effective search space used: 161950 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