Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= BRENDA::P73133 (429 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 563 bits (1450), Expect = e-165 Identities = 269/413 (65%), Positives = 333/413 (80%), Gaps = 1/413 (0%) Query: 16 AVTDLSPAAEFKTADFDTYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLG 75 A D + A+ F T FD VM TYGRFP+A+ RG+G +WDT+G+SYLDFVAGIATCTLG Sbjct: 8 AAVDAAIASPFSTDAFDACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLG 67 Query: 76 HAHPALVRAVSDQIQKLHHVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIK 135 HAHP LV A+SDQI+KLHHVSNLYYIPEQG+LA W+ +SCADRVFFCNSGAEANEAAIK Sbjct: 68 HAHPELVDAISDQIRKLHHVSNLYYIPEQGQLAAWLTANSCADRVFFCNSGAEANEAAIK 127 Query: 136 LVRKYAHTVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDI 195 L RK+ +TVL+ E P+ILTA+ASFHGRTLA +TATGQPKY + F PLV GF YVPYND+ Sbjct: 128 LARKHGNTVLE-AENPIILTAQASFHGRTLAAVTATGQPKYHKGFQPLVQGFRYVPYNDL 186 Query: 196 RSLENKVADLDEGNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQV 255 +LE +A+LD VAAI LEPLQGEGGV PGD AYF+ VR++CDQ +LL+ DEVQV Sbjct: 187 AALEATLAELDAAGETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQV 246 Query: 256 GVGRTGKLWGYEHLGVEPDIFTSAKGLAGGVPIGAMMCKKFCDVFEPGNHASTFGGNPLA 315 G+GR+G+LWGYE+LG+EPD FT AKGL GGVPIGA++ K C++ + G HASTFGGNPLA Sbjct: 247 GMGRSGQLWGYENLGIEPDAFTVAKGLGGGVPIGALLVKASCNILQAGEHASTFGGNPLA 306 Query: 316 CAAGLAVLKTIEGDRLLDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAES 375 C AGLA+ + +E D+LL NVQARGEQLR+GL E+ ++YP L VRGWGLINGL + + Sbjct: 307 CRAGLAIAQVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDP 366 Query: 376 SLTSVEIVKAAMEQGLLLAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAIATL 428 ++T + +VKAA+EQGLLL PAG +V+RFVPPL+V+ AEI +A+ + +A+ + Sbjct: 367 NVTPIALVKAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTERALLAI 419 Lambda K H 0.320 0.137 0.405 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: 576 Number of extensions: 18 Number of successful extensions: 2 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: 429 Length of database: 422 Length adjustment: 32 Effective length of query: 397 Effective length of database: 390 Effective search space: 154830 Effective search space used: 154830 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 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