Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_078428470.1 BK574_RS09735 aminotransferase class V-fold PLP-dependent enzyme
Query= CharProtDB::CH_004890 (393 letters) >NCBI__GCF_002019605.1:WP_078428470.1 Length = 394 Score = 603 bits (1556), Expect = e-177 Identities = 294/393 (74%), Positives = 344/393 (87%) Query: 1 MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60 M+LAKRVS LTPS+TLAITAKAK L+ GHDVIGLGAGEPDFNTPQ+IIDAAV+SM EGH Sbjct: 1 MRLAKRVSTLTPSSTLAITAKAKALREQGHDVIGLGAGEPDFNTPQYIIDAAVKSMEEGH 60 Query: 61 TKYTPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIP 120 TKYTPSGGL++LK++I KFK DQNI Y ++IIVC+GAKHALYTLFQ ILDE DEVIIP Sbjct: 61 TKYTPSGGLSKLKDAIIGKFKDDQNITYSANEIIVCSGAKHALYTLFQAILDEGDEVIIP 120 Query: 121 TPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMY 180 TPYWVSYPEQVKLAGG PVY+EG E N FK++ +QL+ AI +KTKA ++NSPSNPTG MY Sbjct: 121 TPYWVSYPEQVKLAGGNPVYIEGKESNEFKVTVDQLEAAINDKTKAFILNSPSNPTGSMY 180 Query: 181 TEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHS 240 +E+E+ ALG+VCL+HDILIVSDEIYEKL Y G H+SIAQLS+ LKEQTVIINGVSKSHS Sbjct: 181 SEDEMKALGDVCLKHDILIVSDEIYEKLVYDGAVHISIAQLSNELKEQTVIINGVSKSHS 240 Query: 241 MTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300 MTGWRIGYAAG+ ++IKAMTNLASHSTSNPT+ AQYG IAAY +E+MR+AFE RL Sbjct: 241 MTGWRIGYAAGNSEVIKAMTNLASHSTSNPTANAQYGTIAAYTEDDGSVEKMRQAFEERL 300 Query: 301 NTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSG 360 + +Y +LI IPG SCVKP+GAFYLFPNAKEAA CGF +VD++V ALL++EKVA+VPGSG Sbjct: 301 HKVYDQLIAIPGLSCVKPKGAFYLFPNAKEAASICGFDNVDDWVTALLDKEKVALVPGSG 360 Query: 361 FGSPENVRLSYATSLDLLEEAIERIKRFVEKHS 393 FG+PENVRLSYATSL+ ++EA+ERI RF+EK S Sbjct: 361 FGAPENVRLSYATSLEAIQEALERIARFIEKKS 393 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: 591 Number of extensions: 25 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 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