Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_053938968.1 WG78_RS16665 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_001294205.1:WP_053938968.1 Length = 427 Score = 203 bits (517), Expect = 8e-57 Identities = 129/339 (38%), Positives = 194/339 (57%), Gaps = 21/339 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133 L D +G +ID GG + N GH +PV+ +AV+ QL + HS + P + LA+ L Sbjct: 35 LWDEEGHRYIDFAGGIAVLNTGHAHPVITAAVKQQL-EAFTHSCYQVVPYASYVELAERL 93 Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 +TPG K + F ++G E+VE A+K+A+A G+ IA +G FHG+++ ++ T Sbjct: 94 NQVTPGDYAKKTAFFSTGAEAVENAIKIARA---ATGRSGVIAFAGGFHGRTMMGMALTG 150 Query: 193 K-STFRKPFMPLLPGFRHVPFGN------IEAMRTALNECKKTGDD---VAAVILEPIQG 242 K + ++ F P H PF N +E AL + KT + VAA+ILEP+QG Sbjct: 151 KVAPYKIGFGPFPGEVYHAPFPNALHGVTVEQSLKALGDLFKTSIEPRRVAAIILEPVQG 210 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG + PP + A+R+LCDE G ++I DE+Q+G GRTGK+FA +H +V PD++ +AK+L Sbjct: 211 EGGFYVAPPELMQALRRLCDEHGIVLIADEIQSGFGRTGKLFAMQHYSVAPDLMTMAKSL 270 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 GG P+ A E+ P T+ GNPLA AAA A ++++ + +LPA+ + Sbjct: 271 AGG-YPLSAVTGRAELMDA--PAPGGLGGTYAGNPLAIAAAHAVLDLMQQDDLPARGQAL 327 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG 401 GD L+ +L P L E RG G ++A EF+D G Sbjct: 328 GDQLVATLNELKPAVPQLA-EVRGLGAMIAAEFLDPATG 365 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: 442 Number of extensions: 21 Number of successful extensions: 6 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: 427 Length adjustment: 32 Effective length of query: 427 Effective length of database: 395 Effective search space: 168665 Effective search space used: 168665 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 24 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