GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Dechlorosoma suillum PS

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  225 bits (573), Expect = 2e-63
 Identities = 138/387 (35%), Positives = 210/387 (54%), Gaps = 24/387 (6%)

Query: 23  VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82
           +  +  L+   G+G+ + D +G  Y+D V G+ V  LGHG+P +VEA+  QA  L+    
Sbjct: 17  ITQRPQLVFAEGRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLIN--- 73

Query: 83  TLPTPMRGEFYRTLTAILPPEL------NRVFPVNSGTEANEAALKFARA-----HTGRK 131
             P+P    FY   +  L   L      +RVF  ++G EANE A+K AR        G  
Sbjct: 74  --PSPA---FYNEPSLKLAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAH 128

Query: 132 KFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVIL 191
           + +    GF GRT+ ++S + +P +   F P V        ND++++   ++E T A++L
Sbjct: 129 EIITFAGGFHGRTLATMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIML 188

Query: 192 EPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILT 251
           EP+QGEGGV PA+ EFL+  R+I  ++G LLI+DE+QTGMGRTGK FA +H GI PDI+T
Sbjct: 189 EPIQGEGGVVPASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMT 248

Query: 252 LAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAA 311
           L K +GGGVPL A + +E V      G  G T+ GNPL  A G A +  L         A
Sbjct: 249 LGKGIGGGVPLSALLAKESVC-CFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVA 307

Query: 312 ELGPWFMEKLRAIPSP-KIREVRGMGLMVGLELKEKAAPYIARLEKE---HRVLALQAGP 367
             G +    L+ +     +R  RG GL+  L L ++  P I    +E     +L     P
Sbjct: 308 AKGEYLGAGLQRLSDRLGLRGERGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRP 367

Query: 368 TVIRFLPPLVIEKEDLERVVEAVRAVL 394
            ++RF+P L + +E++++++  +  +L
Sbjct: 368 HLLRFMPSLTVSREEIDQMLAWLEELL 394


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: 422
Number of extensions: 26
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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