Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_020174243.1 A3OQ_RS0104875 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000385335.1:WP_020174243.1 Length = 413 Score = 167 bits (424), Expect = 4e-46 Identities = 113/370 (30%), Positives = 187/370 (50%), Gaps = 22/370 (5%) Query: 34 VIGFGAGEPDFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAEKLLK------ENK 87 +I GE D P F+ EA I ++ G+T Y GIPELREAIA + + N Sbjct: 46 LIPLWVGEGDLPAPGFVVEAMIGSIEAGETFYTHQRGIPELREAIARYMARIHSKPFANS 105 Query: 88 VE-YKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVPVEVPLK 146 E + P V+ G + + + GD+VL+ +P W + ++ G +E+PL+ Sbjct: 106 AEPFTPKRFFVTVGGMHAVQIAIRLLAGAGDDVLVLTPAWPNFEGALKVSGARLIEIPLQ 165 Query: 147 KEKG------FQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIF 200 + + L L+ + VT K +V+NSP+NPTG V E+L + F ++ Sbjct: 166 TKMDSTGRQIWSLDLDQLTAAVTPAAKVLVVNSPSNPTGWVATREDLSALLAFARRHDLW 225 Query: 201 IISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVACPEEYAKV 260 II+DE Y + + S DE + F + +FSK+++MTG RIG++ P + ++ Sbjct: 226 IIADEIYGRISFDGGRAPSFHDVMDEEDRVLF-IQSFSKNWAMTGLRIGWLEAPPCFGEI 284 Query: 261 IASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDTAVEELSKIPGMDVV 320 I +L S S V Q A+ AL+ ++ F N+++ E R + L +I + Sbjct: 285 IENLIQYSTSGVAVPLQRAAIAALEEGEA-FFQNQLKRLAESRA-ILCDGLRRIDRVRFA 342 Query: 321 KPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFGAPG--FLRLSYALSEE 378 +P+GAFY+F E + +L+ +++A V V PG+AFGA G ++R+ +A Sbjct: 343 EPQGAFYLF----CTIEGVTDTRELAFRWVDEAGVGVAPGTAFGAGGRDYVRICFARDPA 398 Query: 379 RLVEGIRRIK 388 R+ E +RRI+ Sbjct: 399 RIAEAVRRIE 408 Lambda K H 0.317 0.135 0.383 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: 362 Number of extensions: 16 Number of successful extensions: 6 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: 394 Length of database: 413 Length adjustment: 31 Effective length of query: 363 Effective length of database: 382 Effective search space: 138666 Effective search space used: 138666 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 (21.6 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