Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012968507.1 KVAR_RS15690 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000025465.1:WP_012968507.1 Length = 402 Score = 385 bits (989), Expect = e-111 Identities = 193/397 (48%), Positives = 258/397 (64%) Query: 4 LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63 +A + V+PS T +S + R L+A G+ VI LG GE DF TP +I A I+AI +TK Sbjct: 6 IARRMQSVRPSPTAVISDQVRALEAAGKPVINLGEGELDFATPAHISYAGIEAIVHHQTK 65 Query: 64 YTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAP 123 YT VSG L+EAIA KF R+N L Y + I G+G KQ++FNAF+ATL+ G +V+IPAP Sbjct: 66 YTAVSGTAALKEAIAAKFARDNQLHYRPQEIIAGSGAKQLIFNAFLATLDAGQQVIIPAP 125 Query: 124 YWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSH 183 YWVSYP+MV+L G PV VP ++N +KL E L A+TP T+W + NSP NP+GA YS Sbjct: 126 YWVSYPDMVSLADGEPVIVPCDEQNGWKLTPEQLATALTPSTRWLILNSPGNPTGAIYSE 185 Query: 184 EELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAM 243 +EL+AL VL +P V V+ DD+YE L Y + F T + P + RTLT+NGVSK++AM Sbjct: 186 QELRALAAVLADYPQVLVMADDIYEPLRYDNIPFTTFAQAAPQMVSRTLTVNGVSKSHAM 245 Query: 244 TGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRD 303 TGWR+GYA GP LI AM ++Q Q TS +SI+Q AAV ALN +F + RR Sbjct: 246 TGWRLGYAGGPQWLIAAMQILQSQSTSNPSSISQAAAVAALNHSANFFDGWLNVLDKRRQ 305 Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363 V+ M+ G+S P+GAFYV+ +C L+G+ P G+++ D + LLE VAV+ Sbjct: 306 QVLGMIAATDGLSATAPQGAFYVFANCQALMGRMTPGGEILRNDSALANWLLEQTQVAVL 365 Query: 364 HGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 HGSAFG+ RI+YA + LL +AC+RI CA R Sbjct: 366 HGSAFGMPGYLRIAYAIEDGLLTQACQRIAGACAQLR 402 Lambda K H 0.318 0.134 0.402 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: 434 Number of extensions: 17 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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