Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate WP_013450865.1 CALNI_RS03705 aspartate aminotransferase family protein
Query= curated2:B7LZM2 (459 letters) >NCBI__GCF_000183405.1:WP_013450865.1 Length = 386 Score = 210 bits (534), Expect = 7e-59 Identities = 128/381 (33%), Positives = 208/381 (54%), Gaps = 20/381 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTVAA 135 L D G++++D G + N+GH N + + Q A S +P++ +A+ ++ Sbjct: 23 LFDENGKKYVDFATGIAVTNLGHSNKEIAEIICRQSATLMHTSNLYKNPIQEEVAQIISD 82 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATA 192 L+ G FFCNSG E+ EAALKLA+ Y + + ++ I +FHG++ L+AT Sbjct: 83 LSFGCKV--FFCNSGAEANEAALKLARIYGNKKHNGKRYKIITMVNSFHGRTFATLAATG 140 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 + +K F P L +H+PF +I+A A+ + AV++E IQGEGGVI G Sbjct: 141 QEKVKKGFEPTLDFIKHIPFNDIDAFEKAIEP------ETVAVVMEVIQGEGGVIPAKEG 194 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312 YL AVR++C E L+I DEVQTG+GRTG++F + +V+PDI LAKALG G PIGA Sbjct: 195 YLDAVRRICFEKDILLIFDEVQTGIGRTGEVFGYQLYDVKPDIFTLAKALGNG-FPIGAM 253 Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372 +A E+ L +P H +TFGGN L CA A + + +++ ++KG+ L + + Sbjct: 254 VAKTEIAEYL--SPGTHASTFGGNYLGCAIAKYVLETVSDRSFLDSVKEKGNYLKNKLKT 311 Query: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432 + + + E RG+GM++ + +D+ +F + VL +N T+RI P L Sbjct: 312 IFGD----MGEIRGEGMMIGVRLIDSISLSDFIDRAHKNGVLTVPAGDN--TVRIYPALN 365 Query: 433 LTIEQCELVIKAAHKALAAMR 453 ++ + ++ +K + + Sbjct: 366 ISYDVLNEGLELINKTIGEFK 386 Lambda K H 0.320 0.136 0.395 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: 398 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: 386 Length adjustment: 32 Effective length of query: 427 Effective length of database: 354 Effective search space: 151158 Effective search space used: 151158 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: 50 (23.9 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