Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate WP_010875176.1 NGR_RS30440 aspartate aminotransferase family protein
Query= SwissProt::Q84P54 (515 letters) >NCBI__GCF_000018545.1:WP_010875176.1 Length = 467 Score = 369 bits (946), Expect = e-106 Identities = 183/423 (43%), Positives = 266/423 (62%), Gaps = 4/423 (0%) Query: 83 DPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQLNTLPFYHSFWNR 142 +P I+E +G + D +G + ID AGL+C +G + +A ++Q L +YHS+ Sbjct: 33 EPTIVETGKGIRIQDARGNQLIDGFAGLYCVNVGYGRTEVAEAISRQAYRLAYYHSYAAH 92 Query: 143 TTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPNKKKFIARA 202 TT L+ L+ M K M+K F+ SGS+AN+TQ KLVWYYNN G+P KKK I+R Sbjct: 93 TTDELAILSDRLVKMAPGK-MSKVFYGMSGSDANETQAKLVWYYNNLRGKPTKKKIISRE 151 Query: 203 KAYHGSTLISASLTGLPALHQNFDLPAPFVLHTDCPHYWRYHLPGETEEEFSTRLAKNLE 262 + YHG +++S S+TG+ H + DLP P + HT PH++ PGETE EFS R A L+ Sbjct: 152 RGYHGCSVVSGSMTGMSFYHDHMDLPLPQICHTGVPHHYWGANPGETEREFSARRAAELD 211 Query: 263 DLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILFIADEVICAFGRLG 322 ++I GP+ + AFIAEPV+G GG+ PPP Y++ IQAV+KK+D+L IADEVI FGR G Sbjct: 212 EMIETLGPDNVGAFIAEPVLGTGGITPPPEGYWEAIQAVLKKHDVLLIADEVITGFGRTG 271 Query: 323 TMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNKLGSFSHGFTYSGH 382 +MFGS Y I+PDL+T+AK L+SAY P+ A +V +V V+ ++++G+FSHG+TYSGH Sbjct: 272 SMFGSQHYGIEPDLITVAKGLTSAYFPLSASIVGEKVYKVLEDGADRVGAFSHGYTYSGH 331 Query: 383 PVACAVALEAIKIYKERNMVERVNRISPKFQEGLK-AFSDSPIIGEIRGLGLILATEFAN 441 P+ A A + I ++ ++ + FQ LK F+ PI+GE+RG+GL+ A EF Sbjct: 332 PIGAAAANAVLDIVEKEDLPGNAREVGGYFQAQLKEKFAQLPIVGEVRGVGLMGAIEFVG 391 Query: 442 NKSPNDHFPPEWGVGAYFGAQCQKNGMLVRVA--GDTIMMSPPFVVTPEELDELIRIYGK 499 ++ F P VGA + G++ R GD + +PP V T EE+DE++ + K Sbjct: 392 DRENKKRFDPLLKVGARVSKAARDRGLIARAMPHGDILGFAPPLVTTKEEVDEIVAMAEK 451 Query: 500 ALR 502 A+R Sbjct: 452 AVR 454 Lambda K H 0.318 0.135 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: 613 Number of extensions: 29 Number of successful extensions: 4 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: 515 Length of database: 467 Length adjustment: 34 Effective length of query: 481 Effective length of database: 433 Effective search space: 208273 Effective search space used: 208273 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