Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_057508494.1 ABB28_RS10050 aminotransferase
Query= BRENDA::O69689 (435 letters) >NCBI__GCF_001431535.1:WP_057508494.1 Length = 436 Score = 342 bits (878), Expect = 1e-98 Identities = 186/393 (47%), Positives = 238/393 (60%), Gaps = 4/393 (1%) Query: 30 LALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPEGTDTRNYGGQHGLPGLRAIFAELL-G 87 +A D+TRG PS EQ+ LS+ +LSLPG + +G D NYGGQ G+P LRA+ A LL G Sbjct: 29 VAFDMTRGLPSDEQIALSHAMLSLPGPAPFDSGDGQDWLNYGGQQGIPQLRALLAPLLLG 88 Query: 88 IAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWIQEQDGIKFLCPVPGYDRHFAITE 147 + G NSSL LMH V + G + PW + ++FLCPVPGYDRHFAI Sbjct: 89 VPATQAAVGGNSSLALMHAAVGLAWRIG-LPGHAPWSDAHE-VRFLCPVPGYDRHFAICS 146 Query: 148 TMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMWTVPVFGNPSGVTYSWETVRRLVQMR 207 GI ++P+PM DGPD++ +E+ VA DP I+GMW VP NP G TYS E +RRL M Sbjct: 147 DHGIALVPVPMGHDGPDMERVEKHVAQDPRIRGMWCVPRHSNPCGATYSAEVLRRLATMH 206 Query: 208 TAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAGNPNRPYVFASTSKITFAGGGVSF 267 AAPDF LF DNAYA+H + + A AGNP+R +F STSK+T G GV+ Sbjct: 207 AAAPDFTLFCDNAYAIHDFAPQALARPGLYDACATAGNPDRVLLFGSTSKMTIPGAGVAL 266 Query: 268 FGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDADGVRLHMLRHQQILAPKFALVAE 327 GGS + W+L +IGPDKVNQ+RHLRFFG+A GV HM +H +L +FA V Sbjct: 267 LGGSARIMDWWLAAQRACTIGPDKVNQVRHLRFFGNAAGVARHMQQHGHLLQQRFAQVQR 326 Query: 328 VLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVALAKDVGIAVTEAGASFPYRKDPD 387 V QRL W+ P GGYFI+L + G ARR V+LA G+ +T AG + DP+ Sbjct: 327 VFAQRLRTPCDVHWSRPAGGYFITLWLPTGCARRVVSLASQAGVRLTPAGTTHCGGTDPE 386 Query: 388 DKNIRIAPSFPSVPDLRNAVDGLATCALLAATE 420 D+ +RIAPS V D A + +A C LLA + Sbjct: 387 DRCLRIAPSRLPVADAARAAEIIAGCVLLACAD 419 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: 581 Number of extensions: 19 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: 436 Length adjustment: 32 Effective length of query: 403 Effective length of database: 404 Effective search space: 162812 Effective search space used: 162812 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