Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_012102402.1 CKL_RS10130 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000016505.1:WP_012102402.1 Length = 426 Score = 207 bits (527), Expect = 5e-58 Identities = 140/398 (35%), Positives = 207/398 (52%), Gaps = 31/398 (7%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134 + D G E++D + G + +GH +P VV AV Q K S L++ P LAK L+ Sbjct: 30 MTDINGDEYLDFVQGIAVNALGHCHPKVVQAVVEQTKKLMNGSFNLVNFPTTLKLAKRLS 89 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAK- 193 +TPG L FF N G E+++ ALKLAKAY + IA G+FHG++LGA + TA Sbjct: 90 EVTPGNLNSIFFSNGGAEAIDGALKLAKAYTK---RPAIIAFKGSFHGRTLGATTITASN 146 Query: 194 STFRKPFMPLL--------PGFRHVPFGNIEAMRT--ALNECKK------TGDDVAAVIL 237 S +RK + P++ P P G E RT LNE + VAA+I+ Sbjct: 147 SKYRKYYEPMVGSVYFSTYPSKDLCPKGFDEKQRTEYCLNELDSLFKYVVAPEMVAAIIM 206 Query: 238 EPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILC 297 EP+QGEGG ++P ++ VR +C + G L+I DE+Q+G GRTGKMFA E+ +V PDI+ Sbjct: 207 EPVQGEGGYVVPTKEFVQGVRDICTKHGILLIFDEIQSGYGRTGKMFAGENFDVVPDIMT 266 Query: 298 LAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPA 357 + KA+ GG +P+ A I+T E+ + +H TTFGGNP+ AAALA + N+ Sbjct: 267 VGKAIAGG-LPMSAVISTPEIMDEW--HAGMHGTTFGGNPVCAAAALAVLEEYKNANILE 323 Query: 358 QAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEF------VDNEIGYNFASEMFRQ 411 G L L +Y + + RG G+++AIEF ++ + F+ Sbjct: 324 NVNNMGAYLRKKLEVLKEKY-SCISDIRGLGLMVAIEFSYGDGTPAGDLFEKVRDKCFKN 382 Query: 412 RVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKAL 449 ++L +R PL +T ++ + I K L Sbjct: 383 KLLTLACGVYGNGLRFAAPLNVTEDEIDKGITIIDKVL 420 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: 426 Number of extensions: 27 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: 426 Length adjustment: 32 Effective length of query: 427 Effective length of database: 394 Effective search space: 168238 Effective search space used: 168238 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