Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 207 bits (526), Expect = 6e-58 Identities = 146/399 (36%), Positives = 204/399 (51%), Gaps = 44/399 (11%) Query: 27 QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYES 84 + E A L +G ++DF AG+AV GH HP LVAA+E Q + H + Y++ E Sbjct: 18 EQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPGQER 77 Query: 85 YVTLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAH---TGRPG---VIAFSGGF 137 +AE++ + A TAFF TGAEA+E +KIAR + GRP ++A +G F Sbjct: 78 ---VAERLIK----ASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGSF 130 Query: 138 HGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAK 197 HGRT T+A G Y GFGP HVPY L+A S+ Sbjct: 131 HGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPY----------GDLEAARGAIGSN---- 175 Query: 198 QVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYA 257 AA++ EPVQGEGG A + +R L D+ G++++ DEVQ+G RTGKLFA + Sbjct: 176 -TAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSG 234 Query: 258 DKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKE 317 PD+M +AK L GG P+ V+ PG G T+ GNPLA+A A AVL+ + Sbjct: 235 IAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAP 294 Query: 318 SLCERANQLGQRLKNTLIDAKESVP-AIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQ 376 ER + L+ L D P AIA VRG G M+ G + + + Sbjct: 295 GFLERVQAVAALLRGRLDDLARRYPGAIAQVRGQGLML---------GLKTVPVNTEFNA 345 Query: 377 RALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKIL 415 + A GLL + GA NV+R + PL I +A+ + A++I+ Sbjct: 346 KLFAAGLLAV--GAGDNVVRLVPPLIIGEAEVERAVEII 382 Lambda K H 0.319 0.134 0.388 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: 436 Number of extensions: 25 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: 421 Length of database: 388 Length adjustment: 31 Effective length of query: 390 Effective length of database: 357 Effective search space: 139230 Effective search space used: 139230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. 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