GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Calditerrivibrio nitroreducens DSM 19672

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_013450502.1 CALNI_RS01845 alanine--glyoxylate aminotransferase family protein

Query= BRENDA::A2V838
         (392 letters)



>NCBI__GCF_000183405.1:WP_013450502.1
          Length = 383

 Score =  162 bits (409), Expect = 2e-44
 Identities = 112/344 (32%), Positives = 178/344 (51%), Gaps = 13/344 (3%)

Query: 25  LLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHC 84
           LL PGP+ +P +++    + MI   + +   I  E++EG++ +F TR  + L+++GSG  
Sbjct: 6   LLSPGPTPVPEKVLLDMAMPMIHHRTSEFSNIFKEVREGLKPIFGTRQDV-LILAGSGTA 64

Query: 85  ALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLA 144
           A+EAA+VN L  GD  LV   G +G+R V+I    G  V  +  + G      +VE  L 
Sbjct: 65  AMEAAVVNTLNEGDKVLVVNAGKFGKRWVEIATTYGLDVITIDIEWGRSVKPDQVESKLI 124

Query: 145 QHKPVLLFLTHG-ESSTGVLQPLDGFGELCH-RYKCLLLVDSVASLGGTPLYMDRQGIDI 202
            H  +   L    E+ST    P++  G++   R + LL+VD + S+G     MD  GIDI
Sbjct: 125 AHPEIKAVLVQASETSTTAYHPIEEIGKIVSLRDETLLIVDGITSVGVYETKMDEWGIDI 184

Query: 203 LYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFKGCDDQPRMYHH 262
           L +GSQKA   PPG +LI+ S+KA K  ++ K++   FYL++K     K    Q      
Sbjct: 185 LITGSQKAFMLPPGLALIALSEKAWK--FTEKSRIPKFYLNLK-----KERKSQLENTTS 237

Query: 263 TIPVISL-YSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTV 321
             P +SL   L+  L ++ ++GL N +++H   A      L A+G +L  KD  +   + 
Sbjct: 238 WTPAVSLIIGLKSVLEIMNKEGLPNVYKRHALCAEATRKGLMAMGFELLAKD--IPSNSA 295

Query: 322 TTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLG 365
           T + +P G+D    V  + +   +   GG     GK+LR+  LG
Sbjct: 296 TGIVLPEGFDGGKFVKLMREKAGLTFAGGQDHLKGKILRVSHLG 339


Lambda     K      H
   0.320    0.138    0.418 

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: 332
Number of extensions: 20
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: 392
Length of database: 383
Length adjustment: 30
Effective length of query: 362
Effective length of database: 353
Effective search space:   127786
Effective search space used:   127786
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: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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