Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 236 bits (601), Expect = 1e-66 Identities = 136/380 (35%), Positives = 213/380 (56%), Gaps = 17/380 (4%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 DT+G+E++D + G +GH +PV+++ V Q+ + S P++ LA+ L + Sbjct: 50 DTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLHHVSNLYYIPVQGELAQWL--IQ 107 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKF---TFIATSGAFHGKSLGALSATAKS 194 +FFCNSG E+ E A+KLA+ Y + T + +FHG++L ++AT + Sbjct: 108 HSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIENPTILTAHASFHGRTLATMTATGQP 167 Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYL 254 + K F PL+PGF +VP+ +I A+ +A+ E K VAA++LE +QGEGG+ Y Sbjct: 168 KYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKRQVAAIMLEALQGEGGIRPGDMTYF 227 Query: 255 TAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIA 314 +R++C+E G L+ILDEVQ GMGR+GK++ E+ ++PDI AK LGGG+ PIGA + Sbjct: 228 KRIREICNEKGILLILDEVQAGMGRSGKIWGYENLGIEPDIFTSAKGLGGGI-PIGAMLC 286 Query: 315 TE--EVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372 +VF P H +TFGGNP ACA ALA + L ++NL A +Q+GD L + Sbjct: 287 KSHCDVF-----EPGSHASTFGGNPFACAVALAVCHTLEQENLLANVQQRGDELRIELKA 341 Query: 373 LAREYPDLVQEARGKGMLMAIEF--VDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPP 430 +A +YP+L E RG G++ +E + + +L+ K +R PP Sbjct: 342 IADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNEGLLIVPA--GPKVLRFVPP 399 Query: 431 LTLTIEQCELVIKAARKALA 450 L +T + + + KA+A Sbjct: 400 LIVTETEVKEAMDLLAKAIA 419 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: 468 Number of extensions: 22 Number of successful extensions: 4 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: 423 Length adjustment: 32 Effective length of query: 427 Effective length of database: 391 Effective search space: 166957 Effective search space used: 166957 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