Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_066600058.1 V473_RS02290 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_001046645.1:WP_066600058.1 Length = 398 Score = 200 bits (508), Expect = 8e-56 Identities = 129/382 (33%), Positives = 193/382 (50%), Gaps = 20/382 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134 L+ +G+ ++D G + +GH +P +V A+ +Q A +H L PL A+ L Sbjct: 25 LIGERGERYLDFASGIAVNLLGHGHPRLVKAIADQAATL-MHVSNLYGMPLGEQFAQKL- 82 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191 + FF NSG E+VE A+K A+ Y G + I+ AFHG++LG +SAT Sbjct: 83 -VDNSFADTVFFTNSGAEAVECAIKTARRYHYANGQAHRHKIISFDNAFHGRTLGTISAT 141 Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251 ++ R F PLLPGF VPF +++A ++ D+ A +LEP+QGEGGV Sbjct: 142 SQPKMRDGFEPLLPGFTVVPFNDLDAALAQID------DNTAGFLLEPVQGEGGVTPSTQ 195 Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311 +L +R+ CD G L+ILDEVQ G RTG FA E V PDI+ +AK +G G P+GA Sbjct: 196 AFLKGLREACDAHGLLLILDEVQCGYARTGTFFAHEQYGVTPDIMAVAKGIGAG-FPLGA 254 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +ATEE + H +T+GGNPLA A +A + +L + G L Sbjct: 255 CLATEEAAKGMVFG--THGSTYGGNPLAMAVGIAVLEEVLADGFLDRVTAMGARLRSALE 312 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 QL + + ++ RG G+++ ++ D F + L+A + +RI PPL Sbjct: 313 QLIPNHDGMFEDVRGMGLMLGVKLKDAHDARAFVGHLRDHHGLLAVSAGQ-NVLRILPPL 371 Query: 432 TLT---IEQCELVIKAARKALA 450 + I +C I A + A Sbjct: 372 VIEESHIAECIEKISAGARTFA 393 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: 440 Number of extensions: 20 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: 398 Length adjustment: 32 Effective length of query: 427 Effective length of database: 366 Effective search space: 156282 Effective search space used: 156282 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