Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 255 bits (652), Expect = 1e-72 Identities = 151/392 (38%), Positives = 221/392 (56%), Gaps = 24/392 (6%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y + L + RG+G RVWD +G Y+D V G LGH +PE+V+A+ Q L + Sbjct: 31 YGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVSNL 90 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTG------RKKFVAAM 137 P +G+ LTA + RVF NSG EANEAA+K AR H + A Sbjct: 91 YYIPEQGQLAAWLTANSCAD--RVFFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQ 148 Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKR------AVDEETAAVIL 191 F GRT+ +++ T +PKY + F PLV+ ++PYND+ AL+ A E AA++L Sbjct: 149 ASFHGRTLAAVTATGQPKYHKGFQPLVQGFRYVPYNDLAALEATLAELDAAGETVAAILL 208 Query: 192 EPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILT 251 EP+QGEGGV P + +A R++ ++ LLILDE+Q GMGR+G+ + +E+ GI PD T Sbjct: 209 EPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENLGIEPDAFT 268 Query: 252 LAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRL----W 307 +AK LGGGVP+GA +++ + G H +TFGGNPLA AG+A + +ER +L Sbjct: 269 VAKGLGGGVPIGALLVKAS-CNILQAGEHASTFGGNPLACRAGLAIAQVMERDQLLANVQ 327 Query: 308 ERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKE--KAAPY-IARLEKEHRVLALQ 364 R +L E + P+ + VRG GL+ GL L+ P + + E +L + Sbjct: 328 ARGEQLRAGLQELVDRYPN-LLAGVRGWGLINGLVLRNDPNVTPIALVKAAIEQGLLLVP 386 Query: 365 AGPTVIRFLPPLVIEKEDL-ERVVEAVRAVLA 395 AG V+RF+PPL++ ++ E + RA+LA Sbjct: 387 AGAEVVRFVPPLIVSAAEIDEALAMTERALLA 418 Lambda K H 0.319 0.137 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: 412 Number of extensions: 20 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: 395 Length of database: 422 Length adjustment: 31 Effective length of query: 364 Effective length of database: 391 Effective search space: 142324 Effective search space used: 142324 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 Aug 03 2021. The underlying query database was built on Aug 03 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