Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19); 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate WP_015886801.1 NGR_RS03310 aspartate aminotransferase family protein
Query= BRENDA::Q94CE5 (504 letters) >NCBI__GCF_000018545.1:WP_015886801.1 Length = 466 Score = 385 bits (988), Expect = e-111 Identities = 198/451 (43%), Positives = 281/451 (62%), Gaps = 8/451 (1%) Query: 55 MLAPFT--AGWQSADLDPLVIAKSEGSYVYDDTGKKYLDSLAGLWCTALGGNEPRLVSAA 112 +L PFT + P ++ +G + D +G++Y+D AGL+C +G + A Sbjct: 15 VLHPFTYLKDYAEGATAPTIVETGKGVRIKDASGREYIDGFAGLYCVNVGYGRTEVAEAI 74 Query: 113 VEQLNTLPFYHSFWNRTTKPSLDLAKVLLEMFTANKMAKAFFTSGGSDANDTQVKLVWYY 172 Q L +YHS+ TT+ L+ L++M + M+K FF GSDAN+TQ K+VWYY Sbjct: 75 ARQAYKLAYYHSYAAHTTEELARLSDRLVKMAPGH-MSKVFFGLSGSDANETQAKIVWYY 133 Query: 173 NNALGRPEKKKFIARKKSYHGSTLISASLSGLPPLHQNFDLPAPFVLHTDCPHYWRFHLP 232 NN G+P KKK IAR++ YHG +++S S++GL H + DLP +L T PH++R LP Sbjct: 134 NNLRGKPAKKKIIARERGYHGCSVVSGSMTGLSFYHDHMDLPVAGILRTGVPHHYRGALP 193 Query: 233 GETEEEFSTRLAKNLEDLIIKEGPETIGAFIAEPVMGAGGVIPPPATYFEKVQAVVKKYD 292 GETEE FS R A+ LE LI+ EGPET+ A IAEPV+G GG+IPPP+ Y+ ++QAV+KKYD Sbjct: 194 GETEETFSERRARELEALILAEGPETVAALIAEPVLGTGGIIPPPSGYWPRIQAVLKKYD 253 Query: 293 ILFIADEVICAFGRLGTMFGCDKYNIKPDLVTLAKALSSAYMPIGAILMSQEVADVINSH 352 +L IADEVIC FGR G MFG D Y + PDLVT+AK L+SAY+P+ A ++S++V +V+ Sbjct: 254 VLLIADEVICGFGRTGAMFGSDLYGMVPDLVTVAKGLTSAYVPLSASIVSEQVYEVMQEA 313 Query: 353 SSKLGVFSHGFTYSGHPVSCAVAIEALKIYKERNIPEYVAKVAPRFQDGVKAFASGSPII 412 + ++G FSHG+TYSGHP+ A A L I + ++P AK +KA +PI+ Sbjct: 314 TPQVGAFSHGYTYSGHPLGAAAANAVLDIVERDDLPGQAAKKGAYLMGRLKAEFEQNPIV 373 Query: 413 GETRGTGLILGTEFVDNKSPNEPFPPEWGVGAFFGAECQKHGMLVRVA--GDGILMSPPL 470 GE RG G++ EFV ++ N PF P VGA + ++ R GD + +PPL Sbjct: 374 GEVRGVGMMAAVEFVPDRGANVPFSPALKVGARISQAARNRNLIARAMPHGDILGFAPPL 433 Query: 471 IISPEEIDELISIYGKALKATEEKVKELKAQ 501 +S EIDE++ I A A +E ++EL AQ Sbjct: 434 TMSEAEIDEMVFI---AKAAVDEVLRELYAQ 461 Lambda K H 0.318 0.135 0.404 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: 607 Number of extensions: 23 Number of successful extensions: 3 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: 504 Length of database: 466 Length adjustment: 34 Effective length of query: 470 Effective length of database: 432 Effective search space: 203040 Effective search space used: 203040 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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