Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_010530795.1 ON01_RS09455 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_004890 (393 letters) >NCBI__GCF_000224785.1:WP_010530795.1 Length = 394 Score = 557 bits (1436), Expect = e-163 Identities = 273/392 (69%), Positives = 321/392 (81%) Query: 1 MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60 M+LA RV LTPS+TLAITAKAKELK+ G+DVIGLGAGEPDFNTP++I+ AA +M G Sbjct: 1 MELANRVKTLTPSSTLAITAKAKELKSQGYDVIGLGAGEPDFNTPEYILKAAGEAMQNGF 60 Query: 61 TKYTPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIP 120 TKYTP+GG+ ELK +IA KF+RD + Y +IIV TGAKHALYTLFQV+L++ DEVI+P Sbjct: 61 TKYTPAGGITELKQAIANKFRRDNGLTYTTEEIIVTTGAKHALYTLFQVLLNKTDEVIVP 120 Query: 121 TPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMY 180 PYWVSYPEQ+KLA GKPV++ E+N FKI+PEQL+ AIT KTKA++INSPSNPTG+MY Sbjct: 121 APYWVSYPEQIKLAEGKPVFINAEEKNAFKITPEQLEAAITPKTKAVIINSPSNPTGMMY 180 Query: 181 TEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHS 240 +EEL LGE+CL+H+ILIVSDEIYEKL Y HVS+A++S +LK+ TVIINGVSKSHS Sbjct: 181 NQEELQQLGEICLKHNILIVSDEIYEKLIYTSDNHVSMAEISSQLKDHTVIINGVSKSHS 240 Query: 241 MTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300 MTGWRIGYAAG DIIK MTNLASHSTSNPTSIAQY A+AAYN +P EMRE F RL Sbjct: 241 MTGWRIGYAAGPADIIKPMTNLASHSTSNPTSIAQYAALAAYNTDEDPNAEMREIFSERL 300 Query: 301 NTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSG 360 +Y L +IPG SCVKP+GAFY+FPN +EA GF VD++VKALLEEEKVA+VPGSG Sbjct: 301 ELLYDLLTDIPGISCVKPKGAFYVFPNVREAVSQNGFDTVDDWVKALLEEEKVALVPGSG 360 Query: 361 FGSPENVRLSYATSLDLLEEAIERIKRFVEKH 392 FGSPENVRLSYA S D L+EA RIKRF+ H Sbjct: 361 FGSPENVRLSYAVSADSLKEAATRIKRFILNH 392 Lambda K H 0.313 0.131 0.370 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: 578 Number of extensions: 22 Number of successful extensions: 1 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: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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