Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__PV4:5210744 Length = 426 Score = 203 bits (517), Expect = 8e-57 Identities = 120/334 (35%), Positives = 188/334 (56%), Gaps = 20/334 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133 L D +G+ +ID G + N GH +P VV+AV+ QL H+ +++P + LA+ L Sbjct: 34 LWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFS-HTCVMVNPYESAVALAEQL 92 Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 + PG K + F +G E+VE +K+A+A+ RG IA +G FHG++ ++ T Sbjct: 93 NRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRG---VIAFNGGFHGRTNLTMALTG 149 Query: 193 KST-FRKPFMPLLPGFRHVPFG------NIEAMRTALNECKKTGD---DVAAVILEPIQG 242 K T ++ F P H P+ +++ A+ K DVAA+++EP+QG Sbjct: 150 KITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFKVDIAPCDVAAIVVEPVQG 209 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG PP +L A+R LCD+ G ++++DE+QTG GRTGKMF+CEH V+PD++ +AK + Sbjct: 210 EGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMFSCEHAGVEPDLMTMAKGI 269 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 GG P+ A + E+ P T+GG+P+ C AALA + V+ E+ L +A + Sbjct: 270 AGG-FPLAAVVGKSEIMDAPL--PGGLGGTYGGSPVGCVAALAVLEVMQEEQLVERAVKI 326 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFV 396 GD L +YP L+ E R +G ++A+E V Sbjct: 327 GDSFNQALSALKEQYPQLIGEVRNQGAMIAMELV 360 Lambda K H 0.320 0.135 0.393 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: 474 Number of extensions: 25 Number of successful extensions: 5 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: 459 Length of database: 426 Length adjustment: 32 Effective length of query: 427 Effective length of database: 394 Effective search space: 168238 Effective search space used: 168238 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