Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 202773 SO3678 conserved hypothetical protein (NCBI ptt file)
Query= reanno::pseudo6_N2E2:Pf6N2E2_80 (394 letters) >FitnessBrowser__MR1:202773 Length = 489 Score = 147 bits (371), Expect = 6e-40 Identities = 123/395 (31%), Positives = 188/395 (47%), Gaps = 57/395 (14%) Query: 1 VIGAGYTGLSSALFL--LENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDVIERSVG 58 +IGAGY+GL +A +L + V +LEA +G GASGRNGG ++ S+S D+ + + G Sbjct: 33 IIGAGYSGLWTAYYLKQYQPNLSVAILEADTIGQGASGRNGGWLMGSFSGDVAYLNQLQG 92 Query: 59 PQQAQLLGNMAFEGGRIIRERV---AKYQIQCDLKDGGVF--AALTAKQMGHLESQKRLW 113 +++L+ + +II E AK+ I CDL GG AA +Q+ +++++ W Sbjct: 93 --ESRLMAKALIQ--QIIAEVAAVCAKHHIDCDLHHGGNLRVAARYPEQLANIQAELAQW 148 Query: 114 ER--FGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIY 171 R FG + LD+ + + V+ + IHP L G A V++LG I+ Sbjct: 149 RRQGFGEADIRWLDKTELDKQVSMAHGQAALYTPHCARIHPAKLVCGLADVVQNLGVKIF 208 Query: 172 EQSPAVRIER--GASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATE 229 EQ+P IE A +HTP+G RA ++ A YL L EL ++P + +IATE Sbjct: 209 EQTPVTHIEHWGAAQTRLHTPKGSARAAIVVPAVEGYLRQL-GELGRFTLPVQSLLIATE 267 Query: 230 PLGDELAHSL-LPQDYCVEDCNYLLDYYRLTGDKRLIFG--GGVVYGAR----------- 275 PL DE+ + L D + ++ Y + + D RLIFG GG +GA+ Sbjct: 268 PLTDEMWQDIGLANRATFSDASRIVTYGQRSPDNRLIFGARGGYGFGAKVRTEFGFNREC 327 Query: 276 --------DPANI---EAIIRPKMLKA-FPQLKDVKIDYAWTGNFLLTLSRLPQ------ 317 DP + E R ++L A FPQL DV+I + W G L P Sbjct: 328 FNAQSPASDPQSALKGEFGFRYQLLLALFPQLADVQITHGWGGTLALARQFAPHAIYDKN 387 Query: 318 --VGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEAL 350 +G +G G G GV +L + L + + Sbjct: 388 VGLGLIG-------GYGGEGVGAANLFARTLVDLI 415 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: 477 Number of extensions: 34 Number of successful extensions: 8 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: 489 Length adjustment: 32 Effective length of query: 362 Effective length of database: 457 Effective search space: 165434 Effective search space used: 165434 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