Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_015943022.1 DHAF_RS03890 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000021925.1:WP_015943022.1 Length = 399 Score = 224 bits (572), Expect = 3e-63 Identities = 138/376 (36%), Positives = 211/376 (56%), Gaps = 21/376 (5%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL-DPLRAML 129 G T+ D +G++++D + G + ++GH +P VV A+Q Q A++ LH+ L P + L Sbjct: 30 GKGTTVWDIEGKQYLDFVTGLAVSSLGHSHPAVVEAIQKQ-AEEILHTSNLYWIPNQIAL 88 Query: 130 AKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLG 186 A+ L + FFCNSG E+ EAA+K+A+ Y K+ + +FHG++L Sbjct: 89 AEKL--VEHSFADQVFFCNSGAEANEAAIKIARKYAKEHYSEDKYEILTLVNSFHGRTLA 146 Query: 187 ALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGV 246 L+AT ++ ++K + PL GF +VP ++ + +N VAAV+LEPIQGEGGV Sbjct: 147 TLTATGQTKYQKGYAPLPEGFTYVPINDLAQLEEKMNP------KVAAVMLEPIQGEGGV 200 Query: 247 ILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGV 306 +L RKLCD++GAL+I DE+Q G+GRTGK+FA E NV PDI+ LAKALGGGV Sbjct: 201 FPLEVEFLAKARKLCDDYGALLIFDEIQVGLGRTGKLFAYEWSNVVPDIMTLAKALGGGV 260 Query: 307 MPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML 366 PIG +A E+V S P H +TFGGNPLA A A ++VL E+ +++ Sbjct: 261 -PIGVMLAKEKVASTF--KPGDHASTFGGNPLATAVGCAVMDVLTEEGFLEDVQKRAQYF 317 Query: 367 LDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIR 426 ++LA +Y E RG+G ++ + +G + +L+ K +R Sbjct: 318 KQELQKLADKY-QTGTEIRGQGFILGWPL--DRLGAEIVEGAREKGLLI--NFVGGKALR 372 Query: 427 IEPPLTLTIEQCELVI 442 PPL ++ ++ + I Sbjct: 373 FLPPLNVSYQEIDEAI 388 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: 452 Number of extensions: 24 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: 399 Length adjustment: 32 Effective length of query: 427 Effective length of database: 367 Effective search space: 156709 Effective search space used: 156709 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