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_012041530.1 BBTA_RS05880 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000015165.1:WP_012041530.1 Length = 409 Score = 467 bits (1202), Expect = e-136 Identities = 230/388 (59%), Positives = 281/388 (72%) Query: 5 ADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKY 64 A LS + S + V+ A ++K +G++VI LGAGEPDFDTP+ IK AA A+ G TKY Sbjct: 14 AQRLSAIGVSEILKVTGLAAQMKREGQNVIILGAGEPDFDTPEPIKDAAARAMRDGATKY 73 Query: 65 TPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPY 124 T + G PEL+ AI KFKR+N LD+ + V G KQ+LFNA MATL+PGDEV+IP P+ Sbjct: 74 TALDGSPELKAAIRAKFKRDNGLDFAQDEITVSAGAKQVLFNAMMATLDPGDEVIIPTPF 133 Query: 125 WVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHE 184 WV+Y ++VA+ GGTPV VP + N F+L EDL RAITP+T+W + NSPSNPSGAAYS Sbjct: 134 WVTYADIVAIAGGTPVLVPCSEANGFRLSPEDLARAITPRTRWLMLNSPSNPSGAAYSEH 193 Query: 185 ELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMT 244 + + + DVL+KHP VW++ DD+YEH+ Y FRF TPV +EP L RTLT+NGVSKAYAMT Sbjct: 194 QYRPILDVLLKHPSVWLMVDDIYEHIVYDGFRFVTPVAIEPALRNRTLTVNGVSKAYAMT 253 Query: 245 GWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDL 304 GWRIGY AGP LIKAM ++Q Q TS +SI+Q AA+EAL GPQD I FQ RRDL Sbjct: 254 GWRIGYGAGPSALIKAMAVVQSQSTSCPSSISQAAAIEALTGPQDVIADRCRSFQQRRDL 313 Query: 305 VVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVH 364 VV LN +GISC PEGAFY + SCAGLIG+T P G+V+E D F LL GVAV+ Sbjct: 314 VVDALNSIEGISCCVPEGAFYTFASCAGLIGRTTPDGRVVEDDTVFADYLLRAAGVAVIP 373 Query: 365 GSAFGLGPNFRISYATSEALLEEACRRI 392 GSAFGL P FRISYATS A L +AC+RI Sbjct: 374 GSAFGLAPYFRISYATSAAELRDACQRI 401 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: 520 Number of extensions: 19 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: 409 Length adjustment: 31 Effective length of query: 369 Effective length of database: 378 Effective search space: 139482 Effective search space used: 139482 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