GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Sphingomonas koreensis DSMZ 15582

Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase

Query= SwissProt::Q940M2
         (476 letters)



>FitnessBrowser__Korea:Ga0059261_4131
          Length = 398

 Score =  171 bits (434), Expect = 3e-47
 Identities = 130/412 (31%), Positives = 194/412 (47%), Gaps = 50/412 (12%)

Query: 74  YYQKPLNIVEGKMQYLYD-ESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATT 132
           Y + P+    G+  +LY  + G  YLD  AG+ T + GHCHP ++ A+  Q+  L H + 
Sbjct: 9   YARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISN 68

Query: 133 IYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGSL------EMISL 186
           ++        AE L      +   V+F NSG+EA E A+ +AR Y  +        +I  
Sbjct: 69  MFEMPGQNALAERLTTASFAD--TVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGF 126

Query: 187 RNAYHG---GSSNTIGLTA-LNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDH 242
             A+HG   G+ N  G  A L+ +   LP G +H  V+  P   +  +D +         
Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLP-GFVHFAVDNWPALALAIADSA--------- 176

Query: 243 IEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTG-- 300
                    A  + E +QG GGA  +   +L  +       G + I DEVQTG GRTG  
Sbjct: 177 --------TAAVVVEPVQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKL 228

Query: 301 -SHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAG 359
            +H W     D  PDI+ +AK +G+G P+GA + T E AS +   +   T GGNP+  A 
Sbjct: 229 FAHQW---YPDATPDIMALAKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAV 285

Query: 360 GLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRH-DIIGDVRGRGLMVGIELVSDRKDK 418
            +A  + I K +   H  EV  HL   L  +   H  +I ++RG+GL+VG+ LV + +  
Sbjct: 286 AIAAFDEIAKPETLTHAREVAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNR-- 343

Query: 419 TPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALD 470
                         RE  +LV  GG   N  R+ PP+  T  +AD ++D LD
Sbjct: 344 --------AFMAAAREQRLLVAGGG--DNCVRLLPPLTLTVAEADQILDRLD 385


Lambda     K      H
   0.320    0.138    0.412 

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: 429
Number of extensions: 24
Number of successful extensions: 5
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: 476
Length of database: 398
Length adjustment: 32
Effective length of query: 444
Effective length of database: 366
Effective search space:   162504
Effective search space used:   162504
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 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