Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_003173355.1:WP_109969613.1 Length = 384 Score = 235 bits (600), Expect = 2e-66 Identities = 154/389 (39%), Positives = 221/389 (56%), Gaps = 41/389 (10%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 GS T+ D G++++D + G + + GH +P VV A+ Q A+ S P + LA Sbjct: 28 GSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNLFYVPHQGALA 87 Query: 131 KTLAALT--PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGAL 188 K L ++ PG K +FF NSG E++E ALKLA+ G+ FIA G FHG+++G+L Sbjct: 88 KKLVEISGLPGNAK-AFFSNSGAEAMEGALKLARIRT---GRKEFIACEGGFHGRTMGSL 143 Query: 189 SATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVIL 248 + T K R+PFMPL P VP+G+++A++ A+ E + AAVILEPIQGEGGVI+ Sbjct: 144 ACTHKPAIREPFMPLQPFTSFVPYGDVQALKGAITE------ETAAVILEPIQGEGGVII 197 Query: 249 PPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMP 308 PPPGYL VR++CD G L+I+DEVQ+GMGRTG FA + E + PDI+ +AKA+ G P Sbjct: 198 PPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEGIHPDIITMAKAMASG-FP 256 Query: 309 IGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLD 368 +GA +A E L H +TF G P+ACAAALA+I+V + + LP + KG+ Sbjct: 257 MGAIVAREG----LEFGKSEHGSTFAGGPIACAAALASIDV-IGKVLP-EVAAKGERFRA 310 Query: 369 GFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAK---TI 425 L R KG+++ I D+ ++ V G L N + Sbjct: 311 ALAHL---------NPRVKGLMIGITIGDH-------CADVQKECAVHGLLVNCAAHGNL 354 Query: 426 RIEPPLTLT---IEQCELVIKAARKALAA 451 R+ PPLT+T I++ +I AA A+ Sbjct: 355 RLVPPLTITNAEIDKATGIINAAVSKFAS 383 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: 448 Number of extensions: 26 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: 384 Length adjustment: 32 Effective length of query: 427 Effective length of database: 352 Effective search space: 150304 Effective search space used: 150304 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