GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Dinoroseobacter shibae DFL-12

Align alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate 3609943 Dshi_3325 aminotransferase class V (RefSeq)

Query= BRENDA::Q56YA5
         (401 letters)



>FitnessBrowser__Dino:3609943
          Length = 422

 Score =  337 bits (865), Expect = 3e-97
 Identities = 175/392 (44%), Positives = 242/392 (61%), Gaps = 3/392 (0%)

Query: 2   DYMYGPGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGT 61
           D M   GRH L +PGP  +P+ ++RA++    D+R P    + +  L+ +K IF+T    
Sbjct: 26  DPMRKAGRHFLQIPGPSAVPDRILRAISMQTIDHRGPDFADVGQKALKGMKTIFRTDQNV 85

Query: 62  PFLFPTTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGA 121
            F+FP++GTGAWE+AL NT+SPGD ++ +  G F+ LW    K++  N   +E DW  GA
Sbjct: 86  -FIFPSSGTGAWEAALVNTMSPGDTVLMYETGHFATLWQKMAKKIGLNPVFIEGDWRGGA 144

Query: 122 NLQVLASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSIC 181
           + Q +   L +D +H IKA+C+VHNET+TG  + I+ VR  +D   HPALL+VD +S + 
Sbjct: 145 DPQAIEDALRKDTDHEIKAVCVVHNETSTGSVSPIAEVRAAMDATGHPALLMVDSISGLA 204

Query: 182 ALDFRMDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFY 241
           ++ F  D WGVDV ++GSQK L LP GL     S KALE  K++K  + ++DW D +   
Sbjct: 205 SVPFEFDAWGVDVCVSGSQKGLMLPPGLSFNAVSDKALEVAKSAKMQRSYWDWLDMVGPN 264

Query: 242 KLGTYWPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKE 301
             G Y+PYTP   LLYGL  A+D++ EEGLEN+  RH R G ATR AV AWGL+    ++
Sbjct: 265 ATG-YFPYTPGTNLLYGLNEAVDMLHEEGLENVFERHRRHGAATRAAVRAWGLEVLCARQ 323

Query: 302 EWISNTVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLG 361
              S  +TAVM+P               Y++SLG GL+KVA KVFRIGHLG+ N+L L+ 
Sbjct: 324 GQESGVLTAVMMPEGHSADAFRATTLAHYDISLGNGLSKVADKVFRIGHLGDFNDLMLMA 383

Query: 362 CLAGVEMILKDVGYPVVMGSGVAAASTYLQHH 393
            L+GVEM L   G P   G GV AA  +L+ H
Sbjct: 384 TLSGVEMGLAKAGVPHESG-GVQAAMDHLKTH 414


Lambda     K      H
   0.320    0.137    0.419 

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: 442
Number of extensions: 13
Number of successful extensions: 3
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: 401
Length of database: 422
Length adjustment: 31
Effective length of query: 370
Effective length of database: 391
Effective search space:   144670
Effective search space used:   144670
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 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 (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