Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_026607674.1 METAC_RS0114995 aminotransferase
Query= BRENDA::O69689 (435 letters) >NCBI__GCF_000427445.1:WP_026607674.1 Length = 434 Score = 448 bits (1152), Expect = e-130 Identities = 221/416 (53%), Positives = 293/416 (70%), Gaps = 3/416 (0%) Query: 6 LSPQELAALHARHQQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPEGT 64 LS +L AL AR Q Y A + L LD+TRGKP+ EQLDLS+ LL+LPG+ D+ G Sbjct: 7 LSDADLEALRARVQDQYDAFRAQGLKLDMTRGKPAPEQLDLSSGLLALPGNADHFTEAGE 66 Query: 65 DTRNYGGQHGLPGLRAIFAELLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWI 124 D RNYGG GL RA+FA +LG ++ GNNSSL LMHD + +++L G V SPRPW Sbjct: 67 DARNYGGLQGLAEARALFAPMLGAPPDRVVVGNNSSLALMHDCIVWALLKGVVGSPRPWS 126 Query: 125 QEQDGIKFLCPVPGYDRHFAITETMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMWTV 184 +E + + F+CP PGYDRHFAI E G M+P+PM +GPD+D +E L A +PA+KGMW V Sbjct: 127 KEAE-VAFICPSPGYDRHFAICEEYGFRMLPVPMTGEGPDMDAVEALAA-NPAVKGMWCV 184 Query: 185 PVFGNPSGVTYSWETVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAG 244 P + NP+G YS TV RL M+T APDFRLFWDNAY VH LT +++L A+ G Sbjct: 185 PKYSNPTGEIYSAATVERLAAMKTGAPDFRLFWDNAYVVHHLTERRHEILNILEACARVG 244 Query: 245 NPNRPYVFASTSKITFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDA 304 N +R +VFASTSK+T AGGG++FF S N+ W L AGK++IGPDK+NQLRH+RF D Sbjct: 245 NADRAFVFASTSKVTLAGGGLAFFASSSANVKWLLARAGKRTIGPDKLNQLRHVRFLRDE 304 Query: 305 DGVRLHMLRHQQILAPKFALVAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVA 364 G+ M H+ ++APKFA V E L++RL+ + +A WT P+GGYFIS+D TA+R VA Sbjct: 305 AGILRLMDAHRALIAPKFAAVEEALERRLAGTGVARWTRPEGGYFISVDARKETAKRVVA 364 Query: 365 LAKDVGIAVTEAGASFPYRKDPDDKNIRIAPSFPSVPDLRNAVDGLATCALLAATE 420 LAKD G+A+T AGA++P+ +DPDD ++R+AP++PS+ ++R A +G+A C LLA E Sbjct: 365 LAKDAGLALTPAGATWPFGQDPDDSSLRLAPTYPSLEEVRAASEGIALCILLAGIE 420 Lambda K H 0.320 0.138 0.415 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: 543 Number of extensions: 24 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: 435 Length of database: 434 Length adjustment: 32 Effective length of query: 403 Effective length of database: 402 Effective search space: 162006 Effective search space used: 162006 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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