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_011382998.1 AMB_RS02875 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000009985.1:WP_011382998.1 Length = 400 Score = 570 bits (1468), Expect = e-167 Identities = 273/400 (68%), Positives = 325/400 (81%) Query: 1 MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60 M F+AD LS +KPS TIAV+QKA ELKA GRDVIGLGAGEPDFDTPDNIK AA AID+G Sbjct: 1 MPFIADRLSAIKPSPTIAVTQKAAELKAAGRDVIGLGAGEPDFDTPDNIKAAAKAAIDKG 60 Query: 61 ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120 TKY P +G +LR+AIA KFKREN LDYTA Q VG GGK ++FNAFMAT+NPGDEV++ Sbjct: 61 LTKYGPPAGTVDLRQAIAAKFKRENGLDYTADQVTVGVGGKGVIFNAFMATINPGDEVIV 120 Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180 PAPYWVSYP++ + GG PVFVP + FKL+ DL++AITP+TKW V NSPSNP+GAA Sbjct: 121 PAPYWVSYPDIALMFGGKPVFVPCPETAGFKLQPADLEKAITPRTKWLVLNSPSNPTGAA 180 Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240 YS +E+KALTDVL++HPHVW+++DDMYEHL Y DF+F TP +VEP LY+RTLTMNGVSKA Sbjct: 181 YSWDEMKALTDVLLRHPHVWIMSDDMYEHLVYDDFKFCTPAQVEPKLYDRTLTMNGVSKA 240 Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300 YAMTGWR+GYAAGP +IKA++MIQ Q + +SI+Q A+VEALNG QDFI +N +F+ Sbjct: 241 YAMTGWRVGYAAGPAAIIKAINMIQSQSVTHTSSISQAASVEALNGTQDFIPKNAAVFKR 300 Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360 RRDL+V +LNQ GI+C TPEGAFYVYPSCAG+IGK P GKVI D DFV LLE EGV Sbjct: 301 RRDLIVGLLNQCPGITCRTPEGAFYVYPSCAGVIGKKTPDGKVIANDTDFVGALLEAEGV 360 Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 AVV G+AFGL P FRISYATS+A L +A RI+RFC + + Sbjct: 361 AVVQGAAFGLEPYFRISYATSDAALTKAAERIKRFCESLK 400 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: 569 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 09 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