GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Echinicola vietnamensis KMM 6221, DSM 17526

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__Cola:Echvi_0124
          Length = 386

 Score =  216 bits (550), Expect = 9e-61
 Identities = 125/379 (32%), Positives = 210/379 (55%), Gaps = 10/379 (2%)

Query: 9   KVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYS 68
           ++  + +Y F+       +L+ EG  I+++G+G+PD+PP   + + L   + +P  HGY 
Sbjct: 7   RLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPTSHGYQ 66

Query: 69  ASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPT 128
           + +GIP LR+AI  FY++ Y V L P    +  +G+KE   H+ LA L PGD V++PNP 
Sbjct: 67  SYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVLIPNPG 126

Query: 129 YPIHYYAPIICGGDAISVPILPEEDF-PEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTL 187
           YP +     + G  A+   +  E  + P++   +L +L ++     K + +++PH PT  
Sbjct: 127 YPTYSSVTELVGAKAVYYDLKEENQWLPDI--GQLEELAQSGI---KLMWINYPHMPTGA 181

Query: 188 CVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGF 247
               E  + +V  AK+  I +V+D  Y+ +     +P SIL ++GA D+A+EL S+SK F
Sbjct: 182 NASREALEALVTFAKKHQILLVNDNPYSFILTQ--SPISILSIDGAKDIALELNSLSKTF 239

Query: 248 SMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRR 307
           +M GWRV  + G    ++ +  +KS +D G+F  IQ  +I AL       ++   IY +R
Sbjct: 240 NMPGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKR 299

Query: 308 RDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEY 367
           R+ + +   RVG   ++    MFVWAK+  +   ++L     LL E  + ++PG  FG  
Sbjct: 300 REAVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDK--LLYENHIFITPGDIFGSN 357

Query: 368 GEGYVRFALVENEHRIRQA 386
           G GY+RF+L   E+ I++A
Sbjct: 358 GHGYIRFSLCVPENLIQEA 376


Lambda     K      H
   0.322    0.141    0.425 

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: 418
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: 402
Length of database: 386
Length adjustment: 31
Effective length of query: 371
Effective length of database: 355
Effective search space:   131705
Effective search space used:   131705
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 (21.9 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