GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Synechococcus elongatus PCC 7942

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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