Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_028950007.1 Q385_RS0101715 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000619805.1:WP_028950007.1 Length = 388 Score = 194 bits (494), Expect = 3e-54 Identities = 123/377 (32%), Positives = 206/377 (54%), Gaps = 24/377 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L D +G++++D L G + +G+ +P + A+ Q++K S + +AK L+ Sbjct: 30 LYDEKGKKYLDMLSGIAVNALGYNHPKLTDAICQQVSKIIHISNLFYIKPQIEVAKILSE 89 Query: 136 LT-PGKLKYSFFCNSGTESVEAALKLAKAY--QSPRGKFTFIATSGAFHGKSLGALSATA 192 + GK+ FFCNSG ES EA +KL + Y + K+ I G+FHG++L ++ATA Sbjct: 90 NSFGGKV---FFCNSGAESNEALIKLVRRYFYDKKQDKYEIITFEGSFHGRTLATVTATA 146 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 + + + F PL+ GF++ F +I +++ + D AA+++E +QGEGGV Sbjct: 147 QPKYHEGFYPLVGGFKYAKFNDINSVKNLIT------DKTAAILIELVQGEGGVNPADKE 200 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312 ++ + LC E L +DEVQTG+GRTGK+FA +H +QPDI+ LAK LGGGV PIGA Sbjct: 201 FIKDLYNLCKEKDILFTVDEVQTGIGRTGKLFAYQHFEIQPDIISLAKGLGGGV-PIGAI 259 Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372 IA +++ P H +TFGGN L+ AA + +L + + ++ GD L + + Sbjct: 260 IAKDKIAKSFV--PGTHASTFGGNYLSTVAAKVVLEEVLSEGFLDKVQKVGDYLKESLKV 317 Query: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432 YP +G G+++ ++ + +I + ++ L+ GT T+R PPL Sbjct: 318 FG--YP-----VKGLGLMVGMD-LPKDIPAKEVMKKALEKGLIVGTAGE-NTLRFVPPLI 368 Query: 433 LTIEQCELVIKAARKAL 449 +T +Q + + ++ L Sbjct: 369 ITEKQVDEAVDILKEVL 385 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: 385 Number of extensions: 23 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: 388 Length adjustment: 32 Effective length of query: 427 Effective length of database: 356 Effective search space: 152012 Effective search space used: 152012 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