Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_068172105.1 HTA01S_RS13080 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_001592305.1:WP_068172105.1 Length = 454 Score = 297 bits (760), Expect = 5e-85 Identities = 161/423 (38%), Positives = 241/423 (56%), Gaps = 8/423 (1%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 P + +K+ P I+ +G ++WD +G+K+LDG+ GLW +G+ + DA Q+ Sbjct: 18 PMAHPAAMKKAKPDIVARGEGCWIWDVDGHKLLDGVGGLWASNLGHSATAVRDAIVAQLD 77 Query: 82 ELPYYNLFFQTAHPPVLEL-AKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKG 140 ELP+YN F T HP +EL A+ + + P+G+ V F+ GS+ +T L++ R Y ++G Sbjct: 78 ELPFYNTFRGTTHPRAIELSARLVKLMEPDGVASVMFSSGGSDAVETALKLARQYHKLRG 137 Query: 141 QPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPEE 200 + ++ IS GYHG G S+ G T + +PG HI P+ + P E Sbjct: 138 EKDRFKFISLRQGYHGVHFGGMSVNGNTNFRRAYEPLLPGCFHIDTPWLYRNPYTDDPLE 197 Query: 201 FGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVAD 260 G A LE +I+ G DTV AFIAEP+QGAGGVI+PP +YWP +++I K+ +L +AD Sbjct: 198 LGEICAELLEREIVFQGPDTVAAFIAEPVQGAGGVIVPPANYWPLVRKICDKHGVLLIAD 257 Query: 261 EVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEG----GD 316 EV+ GFGRTG FG+ +G+ DM +AKG++SGY+P+G + +V +V N+ Sbjct: 258 EVVTGFGRTGHLFGTRLWGVNADMWCLAKGISSGYVPLGATAISAKVSQVFNDDKTGQAA 317 Query: 317 FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDH-PLVGEVRG 375 HG+TYS HPV AA AL + + E + +Q+RLR+L VG VRG Sbjct: 318 VGHGYTYSAHPVGAAAALATLDQI-EALDVPGNAGRVGAVMQERLRKLEQTCSFVGNVRG 376 Query: 376 VGLLGAIELVQDKATRARYV-GKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEI 434 VGL+ IE+V DKA R + + + GL++R G +I++PPLVI+ EI Sbjct: 377 VGLMLGIEMVDDKALRTPMPRSNDIPARVAKEAYQRGLMVRISGPNLILSPPLVISLEEI 436 Query: 435 DEL 437 + L Sbjct: 437 NHL 439 Lambda K H 0.320 0.140 0.428 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: 565 Number of extensions: 32 Number of successful extensions: 5 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: 454 Length of database: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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: 51 (24.3 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