Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 216 bits (549), Expect = 1e-60 Identities = 142/383 (37%), Positives = 204/383 (53%), Gaps = 34/383 (8%) Query: 28 DLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP-QTLPT 86 D R A +WD EG +ID G V N GH +P++++A++ Q + Q +P Sbjct: 27 DFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPY 86 Query: 87 PMRGEFYRTLTAILP---PELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 E + + P P+ F ++G EA E A+K ARAHTGR +A GF GR Sbjct: 87 ASYVELAERINRLTPGNYPKKTAFF--STGAEAVENAIKIARAHTGRPGVIAFAGGFHGR 144 Query: 144 TMGSLSVTWE-PKYREPFLPLVEPVEFIPY----------NDVEALKRAVDEE-----TA 187 TM +++T + Y+ F P V PY + +EA+K + A Sbjct: 145 TMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIEAKRVA 204 Query: 188 AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVP 247 A+ILEPVQGEGG A +F+R R + E G LLI DE+Q+G GRTGK FA EH+ ++P Sbjct: 205 AIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLP 264 Query: 248 DILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLW 307 D++T+AK+L GG+PL R E+ + GG G T+ GNPLA+A+ +A + +E +L Sbjct: 265 DLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLV 324 Query: 308 ERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKA-----APYIARLEK---E 357 R LG E L+ + S P+I EVRG+G MV +E + A A Y ++++ Sbjct: 325 TRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALN 384 Query: 358 HRVLALQAGP--TVIRFLPPLVI 378 + +L L G VIRFL PL I Sbjct: 385 NGLLLLTCGSYGNVIRFLFPLTI 407 Lambda K H 0.319 0.137 0.403 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: 423 Number of extensions: 23 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: 395 Length of database: 426 Length adjustment: 31 Effective length of query: 364 Effective length of database: 395 Effective search space: 143780 Effective search space used: 143780 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 (21.7 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