GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysJ in Pedobacter sp. GW460-11-11-14-LB5

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein

Query= SwissProt::Q93R93
         (395 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18530 CA265_RS18530 aspartate
           aminotransferase family protein
          Length = 382

 Score =  217 bits (553), Expect = 4e-61
 Identities = 131/372 (35%), Positives = 206/372 (55%), Gaps = 12/372 (3%)

Query: 23  VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82
           VY  +D+ I +  G+ VWDA   +Y+D  GG+ V ++GH NP  V  +  Q   +     
Sbjct: 6   VYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSN 65

Query: 83  TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSG 142
           ++  P++ +    L  +   +  ++F  NSG EANE ALK A  + GRKK +A    F G
Sbjct: 66  SVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHG 125

Query: 143 RTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALK---RAVDEETAAVILEPVQGEGG 199
           RT  +++VT  PK   P +   E V F+P+N+  AL+   +A   E +AVI+E +QG GG
Sbjct: 126 RTSLAVAVTDNPKIVAP-VNQTENVIFLPFNNEIALEETFKAQGNEISAVIIEGIQGVGG 184

Query: 200 VRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGG 259
           ++ A+  FL+  R +  E  A+ I D +Q G GRTG  ++ ++ G+  D+ T+AK +G G
Sbjct: 185 IKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKGMGNG 244

Query: 260 VPL-GVAVMREEVARSMPKGGH-GTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317
            P+ G+++     ++  P  G  GTTFGGN LA AA +A +  +E+  L + A E+G + 
Sbjct: 245 FPVAGISI----ASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYL 300

Query: 318 MEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLV 377
           + +L+     ++ EVRG GLM+G+EL  + A     L   H +   +A P VIR LP L 
Sbjct: 301 IAELKKF--EQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRLLPALN 358

Query: 378 IEKEDLERVVEA 389
           + K   +  + A
Sbjct: 359 LTKAHADEFLAA 370


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: 327
Number of extensions: 10
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: 382
Length adjustment: 30
Effective length of query: 365
Effective length of database: 352
Effective search space:   128480
Effective search space used:   128480
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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