Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_086509348.1 BZY95_RS07615 succinyldiaminopimelate transaminase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_002151265.1:WP_086509348.1 Length = 408 Score = 105 bits (262), Expect = 2e-27 Identities = 114/373 (30%), Positives = 153/373 (41%), Gaps = 33/373 (8%) Query: 37 LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSG-QAVDAE-Q 94 L++G+P P A + + Y G LR IA RRR +D E Q Sbjct: 34 LTIGEPQH-APFAGALATLHAHQLDFARYPATSGIPELRGAIAAWARRRFRLDGLDPERQ 92 Query: 95 VVVLAGAQCALYAVVQCLLNPGD--EVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFR 152 V+ + G + A++A VQ L+ V V P Y YE G + + R+E+GFR Sbjct: 93 VLPVNGTREAIFAFVQAALDRSRPARVAVPNPFYQIYEGATLLAGGQPHYLDCRAESGFR 152 Query: 153 VQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLF 212 + V A + + + L SP NP+GA PRA ++ L L D + SDE YSEL Sbjct: 153 PDFDAVPAEVWREVQILFLCSPGNPTGAVTPRAEFQKLIALADEFDFIIASDECYSELYL 212 Query: 213 DGEHVSPASLPGMA-------DRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALC 265 D + P L A R +SLSK + G R G+V G A L A + Sbjct: 213 DEDAPPPGLLEACAAMGRHDYRRCLVFHSLSKRSNLPGLRSGFVAGDAELIAPFKRYRTY 272 Query: 266 MLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVM 325 +Q A+ TA + A R+AYR + V E LA P L P+ ++ Sbjct: 273 HGCAMSLPLQHASITAWNDE-AHVRANRDAYREKFAAVTEILA--PVLEFPAPEASFYLW 329 Query: 326 VDIRPTGLSAQAFADRLLDRHGVSVLAGEAFG----------------PSAAGHIRLGLV 369 + G +AF L VSVL G G AG IRL LV Sbjct: 330 PAV--PGGDDEAFTRELFAAEHVSVLPGSYMGRPTTGDGRGRADGRGDNPGAGRIRLALV 387 Query: 370 LGAEPLREACRRI 382 EP EA RI Sbjct: 388 AELEPTVEAAGRI 400 Lambda K H 0.322 0.136 0.411 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: 502 Number of extensions: 25 Number of successful extensions: 4 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: 393 Length of database: 408 Length adjustment: 31 Effective length of query: 362 Effective length of database: 377 Effective search space: 136474 Effective search space used: 136474 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 (21.9 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